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Deduction rules for late arrival and absence

Charge salary deductions for late arrival, early leaving, unplanned absence or short hours, priced by how often it happens in a month, and excuse genuine cases.

Admins & HR Updated 27 Oct 2026
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Deduction rules turn attendance policy into payslip deductions. A rule watches one thing — late arrival, early leaving, unplanned absence or short working hours — and charges each occurrence according to its number in the month. For example: 1st–3rd late free, 4th–6th 25% of a day, 7th onwards 50% of a day.

Before you start

  • Attendance must record late marks, early leaving and hours — see How attendance works.
  • You need the Run payroll, edit salary, FnF, deduction rules & adjustments permission.
  • Loss of pay is separate. An absent day already reduces pay through LOP; an Unplanned absence rule is an extra penalty on top.

Create a rule

  1. Go to Payroll → Deduction Rules ( open Deduction Rules).
  2. On the Rules tab, click New rule.
  3. Enter a Rule name, for example "Late coming". It appears on the payslip, such as "Late coming (4 days)".
  4. In Watches, choose Late arrival, Early leaving, Unplanned absence or Short working hours.
  5. Optionally set a threshold, such as Count only when late by at least a number of minutes. Leave it empty to count every day attendance marks as late.
  6. In Applies to, choose Everyone, Departments, Designations or Specific employees.
  7. Build the tiers. For each tier set From and To (leave To empty for "and after"), then Deduct: Nothing (free), % of a day's salary or Fixed amount (₹), and its Value. Click Add tier for more.
  8. Set Effective from and, if needed, Effective until (optional). Keep Active ticked.
  9. Click Save rule.

"% of a day" means a share of one day's salary: monthly gross ÷ your per-day basis on the Payroll settings tab.

Approval comes first

When Deduction approvals is on (the default), every occurrence waits for HR or the owner to Deduct or Cancel — only deducted ones reach the payslip. Waiting ones show Waiting for approval in the monthly report. See Approve or cancel late and fine deductions.

Check and excuse occurrences

  1. Open the Monthly report tab and pick the month and year.
  2. You see each employee charged, the occurrences and the deduction.
  3. To forgive a genuine case (client visit, approved by manager), click Excuse on that occurrence, add a reason and confirm.
  4. Use Undo excuse to reverse it.

An excused occurrence doesn't count, so later occurrences move down a tier. If a draft payroll exists for that month, the employee's draft payslip is refreshed. Once the month's payroll is approved it shows as Payroll finalized and can't be changed.

When rules are applied

Rules are checked whenever a payslip is generated or recalculated. Excuse occurrences before you approve the run.

Next steps

Still stuck? Email info@cybexinnovation.com or WhatsApp +91 89277 73048.