Suspended Youth Fund boss Bruce Odhiambo and CEO Catherine Namuye have been charged with abuse of office, among other offences on Thursday.
The two have been accused of making an unlawful payment of Sh180 million from the Youth Fund to Quorandum Limited for services not rendered.
They are also accused of making false documents of a contract between Quorandum and the Youth Fund for alleged provision of consultancy services.
Odhiambo and Namuye have been charged together with three directors of Quorandum.
The directors are accused of unlawful acquisition of public property and unlawfully receiving Sh115,710,000 from the Youth Fund.
The offences are said to have taken place between November 17, 2014 and May 4, 2015 in Nairobi county.
Magistrate Felix Kombo deferred plea-taking to Friday since the directors were not present in court.
Kombo released Odhiambo and Namuye on a bond of Sh500,000 and ordered them to appear in court on Friday morning to answer to the charges.