Former Board of Control for Cricket in India president Dalmiya is alleged to have "misappropriated" official funds.
The papers filed accuse Dalmiya of a "criminal breach of trust" in events centred on the 1996 World Cup.
Dalmiya said: "There is no truth in the allegations. The BCCI management has a single point agenda to malign me."
Meanwhile, a close associate of Mr Dalmiya, U N Bannerjee has filed a defamation case against the present board vice-president Lalit Modi, reports BBC Sport.
Dalmiya was the most powerful man in Indian cricket for two decades, and helped the board become the world's richest sporting body.
