Custom HR and payroll software for Karnataka hospitals covering salary structure with CTC breakdown, EPF/ESI/TDS/Professional Tax statutory compliance, monthly payroll processing, payslip generation, Form 16, biometric attendance integration, shift management, leave workflows, and employee lifecycle management. Part of the OneCity 120-module Hospital ERP.
Get a Free Demo WhatsApp UsHospital HR management is more complex than most industries. A 200-bed hospital employs doctors on retainer or consultation fees, nurses on shift-based salaries, paramedical staff on fixed pay, housekeeping on contractor rolls, and administrative staff on standard employment. Each employment category has different salary structures, different EPF/ESI applicability, different attendance patterns (shifts, on-call, 24-hour duty), and different leave entitlements. A generic HR and payroll product built for a standard 9-to-5 office workforce cannot handle this complexity correctly without significant customisation.
Modules 19, 20, and 21 of the OneCity Hospital ERP cover the complete hospital HR and payroll stack. Module 19 (HRM & Payroll) handles salary structure configuration, monthly payroll processing, all statutory deductions, payslip generation, bank transfer file creation, and annual Form 16. Module 20 (Employee Management) covers the employee lifecycle from onboarding through separation. Module 21 (Attendance & Leave) manages biometric or manual attendance, shift rotation, leave types, and the monthly attendance summary that feeds payroll processing. Together, these three modules replace the combination of Excel spreadsheets, standalone payroll software, and paper leave registers that most hospitals use.
OneCity Technologies Pvt. Ltd (CIN: U72100KA2009PTC048911), Bengaluru, Mangaluru, Mysuru. We have implemented hospital HR and payroll software for Karnataka hospitals since 2017, across a range of hospital sizes from 30-bed nursing homes with 50 staff to 200-bed multi-specialty hospitals with 400+ employees across multiple pay grades and employment types.
A hospital’s payroll must handle: doctors on retainer vs consultation fee vs revenue share models; nursing staff on three-shift rotation with night duty allowances; on-call allowances for specialists; split attendance months when staff join or leave mid-month; PF applicability thresholds for contract staff; ESI applicability changes as employee salary crosses the ESI ceiling; and variable components like performance incentives for OPD registration staff. Every one of these requires specific configuration in the payroll engine, not manual overrides.
All features from the live OneCity Advanced Hospital ERP, deployed 2026.
Salary structure configured per employee grade: basic, HRA (set as percentage of basic), dearness allowance, special allowance, transport allowance, night duty allowance, and other components. EPF deduction: 12% employee contribution + 12% employer contribution (split between EPF and EPS per current PF rules). ESI deduction: 0.75% employee + 3.25% employer (applicable for employees below the ESI wage ceiling). Professional Tax per Karnataka slab. TDS computed monthly on projected annual income with investment declaration adjustments. Monthly payroll run produces payslip, bank transfer file, PF challan data, ESI challan data, and PT payment data. Annual Form 16 generated for all employees. References: epfindia.gov.in, esic.gov.in.
Employee master with personal details, qualification records, experience history, and certification tracking (NMC registration for doctors, nursing council registration for nurses, pharmacy council for pharmacists). Document upload: Aadhaar, PAN, degree certificates, professional licences. Department and designation assignment with reporting hierarchy. Probation period tracking with auto-confirmation alert. Transfer and promotion history with effective date. Separation processing: resignation, retirement, termination, or death — with full and final settlement calculation. Employee ID card generation. Credential expiry alerts for licences with renewal due dates.
Daily attendance: present, absent, half-day, on-duty (for off-site work), late-coming, early-going. Biometric device integration ready for FingerTec, ZKTeco, and other standard biometric devices. Shift master with morning, afternoon, night, and on-call shift configurations. Shift rotation scheduling for nursing and paramedical staff. Leave types: Casual Leave (CL), Earned Leave (EL), Sick Leave (SL), Maternity Leave (ML 26 weeks as per Maternity Benefit Act 2017), Paternity Leave, Compensatory Off, and Loss of Pay. Leave application and approval workflow. Leave balance dashboard per employee. Monthly attendance summary feeds Module 19 payroll processing automatically.
Module 20’s employee qualification records connect to Module 109 (Credentialing) for medical and nursing staff. Doctor NMC registration numbers, medical council state registrations, and super-specialty qualifications are stored and tracked for expiry. Nursing council registrations for each nurse are maintained with renewal alerts. This is not just HR documentation — it is the compliance record that hospital administration and NABH accreditation require for every clinical staff member. A doctor whose NMC registration has lapsed cannot legally practise; the system flags this before the expiry date, not after.
EPF (Employees Provident Fund) applies to all employees earning up to Rs 15,000 basic wage per month, and is optional (but often extended) for employees above this threshold. The employer contribution of 12% is split: 8.33% to EPS (Employee Pension Scheme, capped at Rs 1,250 per month) and 3.67% to EPF. An additional 0.5% employer contribution goes to EDLI (Employee Deposit Linked Insurance). Monthly ECR (Electronic Challan cum Return) submission to the EPFO portal requires correctly computed contributions per employee. Module 19 generates ECR data in the required EPFO upload format, eliminating the manual computation that causes errors and late payments.
ESI (Employees State Insurance) applies to employees earning up to Rs 21,000 gross per month. Employee contribution is 0.75% of gross; employer contribution is 3.25%. Hospitals are major ESI-covered establishments because their workforce includes a large number of paramedical, housekeeping, and support staff below the ESI wage ceiling. Monthly ESI challan computation, ESIC portal filing, and Form 6 registers are generated from Module 19. Reference: esic.gov.in.
Karnataka Professional Tax applies on a slab basis: Rs 200/month for monthly salary above Rs 15,000. PT is deducted from employee salary and remitted to the Karnataka state government monthly. Module 19 applies PT automatically based on the employee’s gross salary and the Karnataka PT slab schedule.
Off-the-shelf HR products (Zoho People, GreytHR, Keka) handle standard employment reasonably well. The gaps appear in hospital-specific scenarios that these products require manual workarounds for.
Doctor consultation fee processing: A visiting consultant paid on a per-consultation or revenue-share basis is not a salaried employee. Their payment requires a different computation, a different tax treatment (professional fees with TDS under Section 194J rather than salary TDS under 192B), and different documentation. A hospital running visiting consultants through a generic payroll product either over-complicates the payroll or under-reports the consultant payments for TDS purposes.
Nursing shift attendance: A nurse working 8-hour shifts on a 3-shift rotation, with night duty allowance, on-call availability, and overtime for emergencies, has an attendance record that no standard attendance module handles without configuration work. Module 21 is configured for nursing shift patterns from the start, with the shift master, rotation schedule, and allowance triggers built for healthcare deployment.
Multi-location payroll: A hospital group with branches in Bengaluru, Mangaluru, and Mysuru runs three separate payroll entities (separate EPF and ESI registrations) but needs consolidated HR reporting. Module 19 supports branch-wise payroll processing with separate statutory filings and consolidated group-level payroll analytics for the group HR manager.
HR payroll connects to the full 120-module Hospital ERP — employee records link to credentialing (Module 109), scheduling connects to OT and ICU staffing, and cost accounting (Module 106) maps staff costs to departments for service-line profitability analysis. See also the hospital management software overview.
When attendance is tracked on paper registers or Excel and manually fed into a standalone payroll tool, errors accumulate at every transfer: wrong days counted, overtime not captured, shift allowances missed, and leave deductions applied incorrectly. The nurse who worked 6 night duties in a month but only had 4 recorded because the paper register was illegible loses allowance income. The hospital overpays or underpays staff with no audit trail to investigate. Module 21’s biometric attendance feed to Module 19 payroll eliminates manual transfer entirely — attendance data flows directly to payroll computation with no intermediate human step where errors are introduced.
Late or incorrect EPF/ESI filings attract interest and penalties from EPFO and ESIC. The most common errors in hospital payroll: not enrolling new employees within the statutory 30-day window, incorrect PF wage computation when basic is set incorrectly to avoid higher PF contributions, and not updating the ESI wage ceiling for employees whose salary crosses the Rs 21,000 threshold during the year. Module 19 flags new employees for EPF/ESI enrollment at onboarding and tracks ESI applicability changes automatically when salary revisions are processed. This is a compliance posture change, not just a reporting convenience.
A hospital that employs a nurse whose state nursing council registration has lapsed is operating outside the conditions of its clinical establishment licence. A doctor whose NMC registration is not renewed is practising without valid registration. The risk is not theoretical — clinical establishment inspections check staff registration records. Module 20’s credential expiry tracking sends alerts at 90, 60, and 30 days before any professional licence expires, giving the HR and administration team time to follow up with the staff member before the licence lapses rather than discovering the lapse during an inspection.
The HR payroll data in Modules 19-21 is also the foundation for hospital staffing analytics. Staff cost as a percentage of revenue by department tells management whether a department is over or under-staffed relative to its revenue contribution. Overtime hours by department and shift identifies chronic understaffing that is being managed with overtime rather than addressed through hiring. Absenteeism rates by department, shift, and month identify wellbeing or scheduling issues in specific units. Turnover rates by designation and department surface retention problems before they become operational crises.
These analytics are available in the HRM reports from Module 19 and the attendance data in Module 21. For the full financial picture, staff costs from Module 19 feed into cost accounting (Module 106) for department-wise profitability analysis — a service line’s revenue is only meaningful when it is netted against its staffing cost, which requires both the billing data from Module 14 and the payroll data from Module 19 to be in the same integrated system. This integration is why a standalone HR product, however good at payroll processing, cannot replace the HR module in an ERP architecture. For the full investment picture, see our hospital software cost guide.
The nursing roster is one of the most operationally important documents in a hospital and one of the most time-consuming to create manually. A head nurse managing 30 nurses across three shifts, balancing skill mix (at least one senior nurse per shift), night duty rotation fairness, leave requests, training days, and mandatory rest periods between shifts, typically spends 4–6 hours per month on roster preparation. Module 21’s shift master with rotation scheduling supports automated roster generation from the shift parameters, leave approvals already in the system, and skill mix requirements set by the nursing manager. The draft roster is generated by the system and reviewed by the head nurse rather than built from scratch.
For multi-specialty hospitals where nurses rotate between departments (general ward, ICU, OT), the roster connects to the skill competency records in Module 20 — a nurse who has not been trained for ICU nursing cannot be assigned to ICU shifts. This competency-based assignment is the nursing management standard that NABH accreditation requires and that paper-based roster management cannot enforce systematically. The result is a shift roster that meets clinical governance requirements, is fair to staff, and takes a fraction of the time to prepare compared to manual scheduling. This is one area where the ERP investment pays back in measurable time savings per month from the very first pay cycle after go-live. The head nurse’s time recovered from roster preparation is time available for clinical supervision and quality oversight — the activities that actually improve patient care outcomes in a nursing department. For the broader operational context, see our hospital management software page and the hospital software cost guide.
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Yes. Module 19 generates the ECR (Electronic Challan cum Return) file in the format required for upload to the EPFO Unified Portal. The file contains the monthly contribution data per employee: UAN, basic wage, EPF contribution, EPS contribution, and EDLI contribution. The HR team downloads the ECR file from Module 19 and uploads it directly to the EPFO portal without any manual data entry or reformatting.
Module 19 calculates pro-rated salary for partial months based on the actual working days in the month. If an employee joins on the 15th, salary is calculated from the 15th to the end of the month. If they leave on the 20th, full and final settlement calculation covers earned but unpaid salary, pending leave encashment, gratuity (if eligible), and any deductions for notice period shortfall. All statutory deductions are pro-rated for the partial month automatically.
Yes, for standard biometric devices from FingerTec, ZKTeco, eSSL, and Biomax that support TCP/IP data export. The attendance module pulls punching data from the biometric device daily and matches it to the employee master by biometric ID. Where direct integration is not available, the biometric device’s data export (CSV or Excel) can be imported into Module 21 manually. New biometric devices can be deployed as part of the ERP implementation.
Module 21 includes Maternity Leave (ML) as a leave type configured per the Maternity Benefit (Amendment) Act 2017 — 26 weeks for the first two children, 12 weeks for the third child onwards. When a nurse applies for maternity leave, the system records the expected delivery date, calculates the leave period, and marks the employee as on sanctioned leave for payroll and attendance purposes. Maternity leave pay is processed at full salary. The system also tracks the return-to-work date and any additional childcare leave extensions if the hospital’s policy provides them.
Salary revisions are processed in Module 19 with an effective date. The new salary structure is applied from the revision date, and arrears (if the revision is backdated) are computed automatically for the period between the effective date and the current month. Pay revision history is maintained per employee, so the HR team can see every salary change with the effective date and reason. Increment processing for annual increments can be done in bulk by department and grade, or individually per employee. All revised salary structures are reflected in the updated TDS computation for the remainder of the financial year.
Yes. Branch-wise payroll processing runs each branch as a separate payroll entity with its own EPF registration number, ESI registration number, and Professional Tax registration. Each branch produces its own payslips, bank transfer file, PF challan, ESI challan, and PT payment data. The group HR manager sees consolidated payroll analytics across all branches — total headcount, total payroll cost, department-wise staff cost — while each branch HR processes their own monthly payroll run independently. This multi-entity payroll model is the standard for hospital groups with multiple locations.
Yes. Visiting consultants and contractual doctors paid on consultation fees or revenue share are managed as a separate payment category with TDS deduction under Section 194J (professional fees) rather than Section 192B (salary). Their monthly payment summary, TDS computation, and Form 16A generation are separate from the staff payroll run. This distinction is required by the Income Tax Act and avoids the TDS compliance errors that occur when consultant payments are incorrectly processed through the employee salary payroll.
Explore the hospital HR payroll module with EPF/ESI compliance — with screenshots, feature documentation, and implementation details for Karnataka hospitals.
Tell us your staff strength, employment categories (staff nurses, visiting consultants, contract housekeeping), current payroll method, and statutory compliance gaps. Karnataka hospitals with between 50 and 500 staff are our most common HR payroll implementation profile. Whether you are moving from Excel-based payroll to a proper system for the first time, or replacing a standalone payroll product that does not connect to your clinical and financial systems, we configure the HRM modules to your existing salary structures, attendance patterns, and compliance requirements rather than asking you to adapt your operations to generic software templates. Free assessment and fixed-price proposal within 5 business days. On-site assessment available for hospitals in Bengaluru, Mangaluru, and Mysuru.
Request Free Assessment Call +91 99023 30233 Bengaluru: No. 1869, 2nd Floor, 1st Main Rd, Rajajinagar 560010 | Mangaluru: 1st Floor, Mohtisham, Emporium Complex, Kankanady 575002 | Mysuru: Kantharaj Urs Road, Kuvempu Nagara 570023