The Foreign Affairs ministry wasted more than Sh48.2 million paying allowances and rent for diplomats who had been recalled.
The ministry spent slightly more than half of the amount to pay rent for residences whose envoys and staff had vacated.
Auditor-General Edward Ouko says the ministry irregularly paid millions as Foreign Service allowances.
Kenya embassies including US and Moscow paid staff allowances for higher grades.
Ambassador of Kenya to South Sudan was paid Sh15 million perks for three years to June 2016 despite being recalled in 2013 and paid shipment allowance of Sh2.4 million.
Mr Ouko said the Kenyan Embassy in Bangkok, Thailand continued paying rent for the house previously occupied by the former ambassador who returned to Kenya in July 2013. A rent of Sh8.7 million was paid for the property.
Kenyan Embassy in Seoul, South Korea, paid Sh1.1 million for a vacant house while that in Mogadishu, Somalia, settled Sh13.6 million for unoccupied room. It has been paying Sh$250 (Sh25,500) daily for unoccupied room.
“A room, therefore, remained vacant for 554 days but was paid for, resulting in an irregular expenditure of Sh13,697,650,” Mr Ouko said.