Concerns had been raised by Senator Sakaja about the lack of drugs across hospitals that had resulted in patients turning to private facilities.
But appearing before the Senate Committee on Tuesday, NMS director-general Badi said the payment was expected to be done by the end of this month.
Patients seeking health services in Nairobi county hospitals will soon be able to access medicines.
The Nairobi Metropolitan Services has committed to clearing Sh403.1 million pending bills owed to the Kenya Medical Supply Authority.
The outstanding amount relates to supplies earlier made to over 80 health centres and three hospitals.
Concerns had been raised by Nairobi Senator Johnson Sakaja about the lack of drugs across hospitals that had resulted in patients turning to private facilities to purchase expensive medicines.
But appearing before the Senate Committee on Tuesday, NMS director-general Mohamed Badi said the payment would be done by the end of this month.
He said they formed a committee that looked into the issue and came up with the total arrears owed to Kemsa.
“It is true there is no consistent supply of medicines given the pending bills. However, we talked with the Treasury and they agreed to release some funds to pay the debt owed to Kemsa. Once paid, the bottleneck will be solved,” Badi said.
When the NMS took charge, City Hall had owed Kemsa Sh186.1 million. It inherited Sh195.8 million from City Hall. This was for medical items invoiced on March 13, 2020, and delivered to the NMS.
As of August 2020, Sh2.76 million was owed to Kemsa for drugs supplied to Mama Lucy, Mbagathi, Pumwani, Mutuini and Dandora II health centre.
Badi revealed that requisitions for medical supplies are normally done on a quarterly basis.
So far, requisitions were done at the beginning of the fourth quarter of the financial year 2019-20 and at the beginning of the first quarter of the financial year 2021-22.
However, the medical commodities could not be supplied because of the arrears.
Last month, Kemsa acting commercial director George Walukana said they could only supply what had been requisitioned.
He revealed that Kemsa had not received any order from neither the NMS nor the Nairobi county government for the previous 16 months.
According to Kemsa, Sh186.1 million has been outstanding since July 1, 2017. Deliveries for another Sh196 million, whose local purchase order was issued by the Nairobi government in March 2020, were done in April 2020 when NMS was already in office and in charge of the health department. The sum is also outstanding.
Dr Walukana had clarified that they received only Sh59.1 million from the NMS but the money was for the supply of Covid-19-related items.
He said the NMS paid Sh54.2 million on May 17, 2021, and another Sh4.9 million on July 15, 2021.
Dr Walukana added that Kemsa's team, led by acting CEO Edward Njoroge, was seized of the debt issue and reached out to City Hall seeking a mutual and amicable commitment to clearing the bills.
The acting director made it clear that the state agency remains committed to providing reliable, affordable and quality health products, technologies, and supply chain solutions for improved healthcare.