The Auditor General, Nancy Gathangu, said managers at the state body responsible for purchases, the Kenya Medical Supply Authority (Kemsa) violated procurement rules leading to loss of public money.
The government ordered an investigation following a public outcry.
Kemsa has denied that any money was stolen.
The audit report says that Kemsa bosses colluded with companies that were given contracts. Some of the companies were registered around the time the country recorded its first Covid-19 case.
Items were overpriced and some procured in excess and are still at the Kemsa warehouses.
It says the state body also diverted money meant for the universal health coverage programme and purchased Covid-19 items without approval from the ministry.
The auditor general recommended for an independent audit of the transactions. She also urged investigating agencies to probe any criminality in the procurement process.
The report comes after local media reported that Covid-19 donations from Chinese billionaire Jack Ma were stolen, diverted and sold instead of being distributed.