AAPOULSoftware & MiyabiBase
日本語MiyabiBaseAPOUL HUB
Back office

Deducting pay for absence under a monthly salary

A monthly salary does not always mean the same pay after a day off. What to decide if you deduct for absence, why paid leave must never be treated as absence, and why attendance has to separate the categories first.

Checked 2026.10.24Status: In force2 min read

What you will learn
  • When pay can be deducted for absence
  • Five things to decide in the rules
  • Why paid leave is never absence
  • Which categories attendance must separate

The short answer

A monthly salary does not guarantee identical pay after a day's absence. Companies that deduct for absence must set out how in their work rules or wage rules. And a day of paid annual leave must never be treated as an absence. Attendance has to separate worked days, paid leave, absence and leave of absence before anything reaches payroll.

Deductions are allowed, if defined

Some salary schemes never reduce pay for absence; others deduct. That is the company's choice. Not paying for days not worked is generally regarded as acceptable, but the method must be written down and applied to everyone the same way.

Five things to decide

  1. The unit — whole days only, or hours too
  2. The daily rate — salary divided by that month's scheduled days, or by an annual average
  3. Which allowances are included
  4. How it lines up with pro-rating for mid-month joiners and leavers
  5. What happens in a month with many absences

Item 2 is easy to miss: dividing by the month's scheduled days makes the daily rate change month to month, while an annual average keeps it fixed.

Paid leave is not absence

Annual paid leave under Article 39 of the Labour Standards Act is paid. Deducting pay for a day of paid leave is not allowed. The mistake usually happens when attendance has only one kind of "day off". Leave of absence follows the company's own rules and needs its own category too.

Separate the categories in attendance

At minimum: worked, annual paid leave, absence, leave of absence, and company special leave (paid or unpaid). APOUL KINTAI records leave types separately and hands the closed record to payroll.

Summary

If you deduct for absence, define the unit, daily rate, allowances, pro-rating and limits, and apply them uniformly. Never treat paid leave as absence. Consult a specialist when drafting the rules.

Read nextBack officeDeducting pay for lateness and early leave, the same way every timeDeducting pay for lateness or leaving early starts from the time not worked. Taking more than that counts as a disciplinary pay cut, with statutory limits. What to write into the rules, and how attendance should hand it to payroll.
Related

Also worth reading.

Back officeHow overtime pay is calculated, and why attendance must sort it firstOvertime pay is not hours times an hourly rate. Statutory and scheduled hours, overtime, rest-day and late-night categories, the rate beyond 60 hours a month, and how the hourly wage is set — checked against primary sources.2 min readBack officeWhat Breaks When Attendance, HR and Payroll Are SeparatePlenty of companies register the same new hire three times, once each in HR, attendance and payroll. A walk through five situations where that costs real time: typos, leavers who are never removed, transfers, pay changes, and access rights.5 min readBack officePaid leave: what happens when you track it separately from attendanceKeeping paid-leave balances in a spreadsheet or paper ledger, separate from attendance records, means checking two places every time someone applies. Here is what changes when leave lives inside the attendance system itself.5 min read
At APOUL

Making everyday paperwork and information a little simpler.

APOUL builds software to take some of this work off your hands. Everything is in preparation for release; the price, the distribution method and the supported systems will be announced on each product page once decided.

See the productsAll columns