By Pascal Ndegwa - Reporter
Kenya, October 14 ,2026 - Controller of Budget Dr Margaret Nyakang’o in a media engagement on October 13 says the new system has made it harder for government offices to borrow money just to pay workers’ salaries.
The system connects two important tools. One is called IFMIS. It tracks how government money is spent. The other is the Government Human Resource Information System. It handles workers’ pay. When the two systems work together, something important changes.
Before, some government offices (especially counties) could pay workers their take-home salary but hold back the money that was supposed to go to tax, pensions, health insurance and other deductions. They sometimes used that held-back money for other things. Later, when they needed to pay the deductions or cover the full salary cost, they ran short of cash and had to borrow.
Now the systems are linked. When an office processes salaries, the computer pays the worker their net pay and at the same time sends the tax, pension and other deductions to the right places. Everything happens together. This means offices can no longer treat the deductions as extra cash they can use elsewhere.
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Dr Nyakang’o says this change has helped ease the problem of borrowing just to meet the salary bill. The new system started working in July 2026. It does not wipe away old debts that counties still owe. Those remain the counties’ responsibility. But it is meant to stop new problems from growing.
Counties already have more than KSh100 billion in unpaid salaries and deductions from past years. The Controller of Budget hopes that if the new system keeps working well, there will be no new short-term salary arrears by the end of the current financial year.
In simple terms, the government has made it much harder for public offices to pay workers while quietly keeping the rest of the money , and then borrowing to fix the mess later.