Sharad Ghai, arrested by Kenyan police on Wednesday, is accused of conspiring to defraud the KCA of 3.3 million dollars during a four-team tournament in Kenya in 1999.
He is also charged with stealing just over three million dollars from the KCA during the course of 1999.
Ghai denied both charges.
The court set Ghai's bond at two million Kenyan shillings (26,300 dollars). His next court appearance is set for April 21.
The case against Ghai, who took over as the chairman of the KCA in May last year, was instigated by the International Cricket Council which had been due to receive a portion of the proceeds from the tournament.
Kenyan Sports Minister Ochilo Ayacko dissolved the KCA in January over corruption allegations and named a caretaker committee but the sacked administrators won a court order to keep their jobs and the battle for control of the sport continued until last weekend when the African Cricket Association mediated a deal.
The KCA and Cricket Kenya have agreed to merge until fresh elections are held in May.