Stephen Arap Soi, the country’s chef de mission, is facing five charges related to the theft of 25.6m Kenyan shillings ($256,000, £197,000).
Two other top officials denied charges of stealing team uniforms provided by sponsor Nike.
Team Kenya, which won 13 medals at the Games, was dogged by allegations of mismanagement and corruption in Rio.
Mr. Soi is accused of taking $234,000 on a flight from Kenya to Brazil on 20 July without declaring it to customs officials, according to Citizen TV.
Prosecutors say that money was not accounted for at the Olympics.
Mr. Soi was charged with stealing the remainder in smaller amounts on separate occasions.
The National Olympic Committee of Kenya’s Vice-President Pius Ochieng and Secretary-General Francis Kinyili Paul also denied the charges levelled against them.
The next hearing is on 24 October.
Kenya won the most medals of any African country, but was beset by scandals, including athletes not receiving their Nike kits.
The East African nation ended with athletes being stranded in a Rio shanty town, while officials looked for a “cheap flight”.
The government ordered an investigation into the alleged mismanagement on their return.