Francis Paul, the secretary-general of the National Olympics Committee of Kenya (Nock), Pius Ochieng, Nock's vice chairman, and a third man, Stephen Soi, are being investigated for theft, abuse of office and neglect of duty.
The officials are blamed for a series of problems facing Kenya's athletes.
They have made no comment.
Bail for Mr Paul and Mr Ochieng was set at $2,000 (£1,530). Mr Soi had already been released from police custody for medical reasons and his bail will be set on Wednesday.