Police on Monday arrested the head of the National Youth Service over the reported looting of Sh9 billion, the latest in a string of graft scandals to erupt in the country.
The director of the NYS, Richard Ndubai, and the principal secretary of in the youth ministry, Lilian Omollo, were detained in dawn raids.
"The suspects are in custody and we will take them to court," said the head of Kenya's criminal investigations unit, George Kinoti.
The NYS is a paramilitary training institution that has been at the forefront of President Uhuru Kenyatta's plan to combat high youth unemployment.
Enrolment is voluntary, and sees youths receive a stipend while receiving technical training and working on government projects.
With a budget soaring to some Sh250 million a year, the NYS has been plagued by Kenya's endemic corruption, with a first scandal breaking in 2015 after the theft of Sh700 million through inflated pricing and fictitious payments.
The latest scandal — brought to light by suppliers who had not been paid — appears to show how families and friends of powerful politicians ended up receiving millions of dollars in questionable payments.
The media have reported how the NYS paid Sh1 billion for beef in one year — meaning each recruit would have had to consume 66 kilos (145 pounds) of beef a day.
In another example a car tyre was purchased for Sh100 million.
Aside from the top brass at the agency, 17 middle-level and junior level officials are being held.
According to the prosecutor's office, charges will include abuse of office, stealing public funds and forgery, amongst others.
Corruption scandals have in recent days also hit electricity utility Kenya Power — where families and friends of employees were found in an audit to have bagged multi-million dollar contracts.
Fraudulent payments of Sh300 million have also been uncovered at the National Cereals and Produce Board.
In 2017 Kenya fell to 143rd out of 180 countries in Transparency International's annual corruption index.
In March, a damning report from the auditor-general showed government could not account for Sh4 billion in public funds.
Kenyatta has vowed to combat corruption, a refrain weary Kenyans have heard from multiple presidents.
In an editorial in the Saturday Standard, a columnist referred to a 1968 headline in which government vowed to "crush" corruption.
"Since independence government in Kenya has not been about service ... The foremost reward of winning an election would seem to be the opportunity to steal," wrote columnist Barrack Muluka.
"We have sung the anti-corruption song for far too long, we can only be tired of it."