The president of Football Kenya Federation (FKF) Nick Mwendwa has been released on bail pending further investigations.
Mwendwa, who spent the weekend behind bars after his arrest on Friday, was ordered to pay Kshs4 million (approximately $36,000) bail to secure his release.
The bail conditions set by the judge at a court in Nairobi dealing with corruption cases also stipulated that Mwendwa cannot access FKF offices, talk to staff, attend football matches or conduct media interviews.
When he was first taken into custody the FKF spokesman said:"He was not given any reason why he was arrested, so we are still trying to follow up."
Mwendwa has denied any wrongdoing.
A recent report commissioned by Kenya's Sports Ministry recommended that authorities should carry out further investigations into the FKF.
These are intended to establish "the extent to which the misappropriation of funds in FKF may have occurred, with a view of prosecuting those who may be found culpable".
Fifa officials were recently in Nairobi conducting their own audit into the FKF, which Mwendwa has led since 2016.
His detention came two days after Kenya's Sports Ministry created a caretaker committee to run the federation for six months.
On Thursday, football's world governing body advised that Kenya is likely to face an international ban unless the actions of Sports Minister Amina Mohamed are undone.
Fifa disapproves of governmental interference in the running of a member association and has banned countries from all forms of football as a result in the past.
The Confederation of African Football (Caf) has also said that it is "deeply concerned about the situation and the manner in which the situation is unfolding and notes all the allegations that have been made.
"Caf is committed to good governance in African football administration. At this stage, we will not make any further comments until we have full understanding of the entire picture," the statement added.
"Caf together with Fifa are monitoring the situation."