The president of Football Kenya Federation (FKF), Sam Nyamweya, and two other officials are being investigated for "conspiracy to defraud".
Kenya's Office of the Director of Public Prosecutions (ODPP) are looking into the case following a recommendation from the Directorate of Criminal Investigations (DCI).
The case centres on how almost US$170,000, set aside for Kenya's trip to Cape Verde for a 2018 World Cup qualifier in November, was actually used.
A statement from the ODPP says that Michael Esakwa the federation's secretary general and Samson Cherop the acting finance manager are also being investigated.
The ODPP says the police and DCI have recommended the trio "be charged with offences of conspiracy to defraud, stealing by agent and fraudulent false accounting."
The case is now being "independently reviewed and decisions thereon made shortly based on evidence and the law."
The Kenyan football team were delayed in Nairobi for several hours and eventually left less than 24 hours before the second leg of their World Cup qualifier in Cape Verde, which they lost 2-0.
The loss in the second leg in Praia saw the Harambee Stars eliminated from 2018 qualifying losing 2-1 on aggregate.
FKF are due to hold elections in the next few months and Nywamweya is hoping to win a second term as president.