The first charge stated that he conspired with others between April and December 1999 to steal the money, which was set aside for a quadrangular tournament held in Nairobi that year.
The second count charged him with the actual theft.
Further hearings are scheduled for April 21 and June 22.
Three months ago the government disbanded the KCA and installed an interim committee to run the association.
Ghai successfully challenged the move but the government registered a rival body to run cricket in Kenya. Both matters are pending in Kenyan courts.
