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Absence, unpaid leave and attendance in payroll

Salary is reduced for unpaid leave, for absent days entered by hand, and, if the company chooses, for late, early-out and absent days taken from attendance. Three switches on Payroll configuration decide which of these apply.

  • HR & payroll Running payroll
  • 4 min read
  • Updated October 20, 2026

For Payroll officer HR officer Accountant

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The idea

Three kinds of absence can reduce an employee's pay. The pay run adds them up as absent days and takes basic salary plus grade, divided by the days in the month, times the absent days off the salary.

KindApplies whenWhere it comes from
Unpaid leaveDeduct unpaid leave salary is ticked in Payroll configurationApproved leave of an unpaid leave type (How leave works: types, rules, balance and carry-forward)
Manual absent daysAlwaysAbsent day entry
Attendance basedAttendance based payroll system is tickedAbsentee Payroll Deduction, from attendance

Every calendar day of an approved unpaid leave counts, including weekends and holidays in the range.

Absent day entry

  1. Open the tab
    Who
    Payroll officer
    Where
    Other income/deduction › Absent day entry › Add
    What changes
    The form opens.
  2. Fill it in
    What changes
    Choose the Period, the employee (Name), the From date and To date, and tick First day half or Last day half where needed. Absent days is counted for you. Every entry is taken off salary; the list shows Deduct from salary as ticked.
  3. Save
    What changes
    The days are taken off at the pay run for that period. An employee's absence cannot overlap another entry, and it cannot be entered after payroll for the period was generated for that employee.

Absentee Payroll Deduction (from attendance)

Use this when the company deducts for late, early-out and absent days.

  1. Choose the attendance period
    Who
    Payroll officer
    Where
    Other income/deduction › Absentee Payroll Deduction
    What changes
    The list shows, for each employee and date, the Start time and End time of the shift, the In and Out punches and the Payroll status.
  2. Choose the days and the type
    What changes
    Select the rows to deduct. For each row the Deduction type is a late check-in, an early check-out or an absent day.
  3. Save
    What changes
    The chosen days are kept as deductions. Rows already deducted cannot be chosen again.

How much each type is worth:

  • An absent day is 1 day, a half leave day is half a day.
  • A late check-in or an early check-out of more than 15 minutes is a quarter of a day each.

The pay run adds the chosen amounts to the absent days of the month. If you delete a payslip to make it again, select that employee's attendance deductions again first: deleting the payslip removes them.

Showing absence on the payslip

Include Absence Salary decides how it looks. Ticked, the payslip shows the full salary and a separate Absent deduction. Not ticked, the salary lines are already reduced. Apply Leave Impact to PF/SSF ticked means PF, SSF and gratuity are worked out on the reduced salary (Reading a payslip).

Common questions

A late check-in is not on the Absentee Payroll Deduction list.

The list offers a day only when it is an absent day, or when the check-in was more than 15 minutes after the shift started, or the check-out more than 15 minutes before it ended. A day inside 15 minutes is not offered, whatever the grace minutes are.

Does a day of paid leave reduce the salary?

No. Only unpaid leave is taken off, and only when Deduct unpaid leave salary is ticked.

I need to enter an absent day for a month that already has a payslip.

An absence cannot be entered once the payslip for that employee and period exists. Delete the draft payslip, enter the absence, and generate the payslip again (Run the month's payroll). If you use Absentee Payroll Deduction, choose the employee's days there again before you generate.

Related guides

How a payslip is worked out Payroll in Penahak is monthly. The pay run works out each employee's salary, allowances, deductions, provident fund or SSF, CIT… Payroll configuration The company-wide payroll settings in two tabs: General settings (PF or SSF, gratuity, CIT, tax limits, loans, how absence is… Extra income and deduction: one-off items, PF loan, medical discount, previous income Anything that is not part of every month's pay goes here before the pay run: a bonus or a one-off deduction, a PF loan… How attendance is recorded A day is built from the employee's shift, the punches from a device or a manual entry, and the leave, visit and holiday records… How leave works: types, rules, balance and carry-forward A leave rule gives each job type a number of days of each leave type for the attendance year. A request takes first from this… Ask for leave Choose the leave type and dates, say who should approve, and save. Penahak checks the dates, the rule and the balance before it… Run the month's payroll Choose the pay period, tick the checklist, select the employees and generate. Each gets a draft payslip you can view, print or… Reading a payslip The payslip lists income, deductions and net salary for one month, with year-to-date totals and the leave and absence that…

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