The chairman of the Kenya Cricket Association has been accused of stealing �1.75m from their funds. Sharad Ghai pleaded not guilty before magistrates in Nairobi to charges of conspiracy to steal and theft.
Ghai was released on bail and further hearings will take place on 21 April and 22 June.
The case is the latest in a series of setbacks for Kenyan cricket, which was on a high in 2003 after the national team reached the World Cup semi-finals.
Since then, players have been involved in strikes for more money and former captain Maurice Odumbe was handed a five-year ban after being found guilty of receiving money from a bookmaker.
The government tried to dissolve the KCA in January amid claims of financial mismanagement and tried to put a new body called Cricket Kenya in charge.
Ghai successfully challenged the move in court.
But agreement was reached earlier this week for the two to merge and jointly run the game until elections for a new governing body, which will take palce on 21 May.
The plan was thrashed out at a 16-hour meeting, also involving African Cricket Association officials.
"The only way forward is having the two committees working for one objective," said Zimbabwe's Peter Chingoka, head of the ACA delegation.
"The International Cricket Council has been greatly disturbed by the whole scenario," he added.