Doctors and nurses will receive salaries and allowances for the 100 days they were on strike at the end of this month.
On Wednesday, Kisii Governor James Ongwae said county governments have received the funds from the Ministry of Health.
Mr Ongwae, who is chairman of the Human Resource, Labour and Social Welfare Committee at the Council of Governors, said counties have been waiting for the funds from the ministry and will now disburse it at end of the month.
"Doctors should not worry because at the end of this month, their money will have been disbursed," he said.
He spoke as his counterpart in Tharaka Nithi Samuel Ragwa assured doctors in his county that his administration was processing the salaries and that they would be paid out by end of the week.
The county boss said governors have been willing to pay doctors as stated in the return-to-work formula but there has been no money.
On Tuesday, Health Cabinet secretary Cleopa Mailu showcased a Sh3.2 billion payment made to county governments for the same.
The ministry also allocated an additional Sh1.73 billion to cater for allowances of about 24,000 doctors.
Dr Mailu also issued a directive to counties to pay doctors their salaries including those that were withheld when they were on strike.
Mr Ongwae acknowledged that most counties had received the funds to pay for salaries and the new allowances to doctors and nurses.
Dr Mailu warned counties against diverting the funds. "All counties were given the money for personal emoluments and they should pay all pending salaries... you cannot use the money on anything else. It is for staff."