Hundreds of thousands of condoms, mosquito nets and tuberculosis drugs worth $100,000 (£77,000) are alleged to have disappeared from a warehouse operated by the Kenya Medical Supplies Authority (Kemsa).
They are believed to have been stolen and resold on the black market and to private chemists, according to the UN’s Global Fund to fight HIV, TB and malaria.
It also accuses the agency of drastically inflating the price of the medicine, with some drugs being sold for one hundred times the correct cost.
The government agency has not yet commented on the allegations.
Kemsa made headlines in 2020 after revelations of fraud over the procurement of Covid-19 medical supplies.
Tenders worth $78m were said to have been irregularly given to politically connected individuals and businesses.
This prompted President Uhuru Kenyatta to disband its board and top management.
The UN Global Fund, which has disbursed more than $1.4m to Kenya in the last two decades, has recommended further investigation of Kemsa over the lost medicines.