Can Your Employer Deduct Your Salary?

Check the basis for a Kenyan salary deduction, understand the general deduction limit and prepare a clear payroll query with supporting evidence.

4 min readReviewed 1 November 2026
Employee pointing to a paper while discussing a salary query with a payroll adviser.

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A Kenyan employer can make certain deductions from wages, but a payroll label alone does not make a deduction lawful. Check three things separately: the legal basis, the amount and whether money intended for another organisation was actually remitted.

Use the PAYE and net salary calculator for an estimate of ordinary statutory deductions. It cannot decide whether a disputed damage charge, loan recovery or absence deduction is lawful. The employment situations guide provides related payroll explanations.

Start with the reason for the deduction

Section 19 of the Employment Act lists permitted categories with conditions. These include deductions authorised by law or specified instruments, erroneous wage overpayments, qualifying written requests and repayments of employer loans under written agreements. Damage deductions concern wilful default; they are not a blanket permission to charge staff for every accident.

Ask payroll to identify the relevant category and supporting evidence. If the explanation is “company policy”, ask how that policy and the particular charge meet the applicable requirements. Do not assume signing a general handbook authorises every future deduction.

Check the amount separately from the authority

Section 19 sets a general ceiling of two-thirds of wages for the deductions under that section, subject to any prescribed different amount. For employer loans under a written agreement, the repayment deduction cannot exceed 50% of wages remaining after the other section 19 deductions. A deduction below the overall ceiling still needs a lawful basis.

For a simple illustration, if the applicable wages are KES 60,000, two-thirds is KES 40,000, leaving KES 20,000. This is arithmetic, not an assessment of a particular payslip: confirm the relevant wage figure, deduction categories and any applicable exception. Do not treat KES 40,000 as a free allowance for the employer to invent charges.

Separate a wage deduction from a change in pay

A line subtracting money from earned wages is different from a proposed change to contractual salary, or a disagreement about how much salary was earned. Ask which situation applies before comparing figures. Record the period and effective date rather than arguing only about the final bank transfer.

For an absence adjustment, gather attendance records, leave approval and the calculation used. For an alleged overpayment, request a comparison between what should have been paid and what was actually paid. For damage, ask for the incident details, evidence and valuation. These records help test the explanation; they do not establish liability by themselves.

Build a one-page deduction query

  • Name the payroll month and exact deduction label.
  • State the amount and why you cannot reconcile it.
  • Ask for the basis, calculation and relevant agreement or instruction.
  • Attach only the documents needed for the issue.
  • Request a written response and retain the correction trail.

A useful opening is: “My [month] payslip includes KES [amount] for [label]. Please provide the basis and calculation, including the period covered, and explain how this complies with the applicable deduction limits.”

Use the payslip reading guide to distinguish employee deductions from employer contributions shown for information. If the disputed line is income tax, use the wrong PAYE checklist instead of treating all deductions as discretionary charges.

Follow up unresolved deductions

Keep the contract, payslips, bank records and responses together. If payroll cannot resolve the issue, consider your union representative, a labour officer or a qualified employment adviser. Ask what route and time limits apply to your circumstances rather than assuming every wage complaint follows the same process.

Where the money was meant for a third party, check its receipt separately. For example, missing HELB remittances require loan-statement reconciliation as well as an explanation from payroll. A corrected payslip is not proof that the intended recipient has been paid.

Sources and review date

Published and reviewed on 1 November 2026. Use the rules and official instructions applicable to the period concerned.