The charges against Opuni, who was sacked by President Nana Akufo-Addo in January 2017, were laid Wednesday at the High Court in Accra, the capital, Joseph Addo, a spokesman for the office of the attorney-general and the justice ministry, said by phone.
He is alleged to have mismanaged the cocoa sector during his tenure.
Dr Opuni was relieved of his post on January 12, 2017.
Already, the former Director General of the National Communications Authority (NCA), William Tevie and some other officers have been hauled before court for causing financial loss of about Ghc4million which was to be used to procure surveillance equipment for National Security.
A total of 27 charges have been leveled against them, Graphic Online has gathered.
The suit said "Mr. Stephen Kwabena Opuni between November 2014 and November 2015 in Accra in the Greater Accra Region, abeted Seidu Agongo and Agricult Ghana Limited to defraud Ghana COCOBOD of the sum of Ghc 75, 289, 314.72".
The former chief executive officer of Ghana Cocoa Board, Stephen Opuni, has been charged for causing financial losses to the state during his tenure as head of the regulator, according to a justice ministry official.
In fact, the state accuses Seidu Agongo of "manufacturing the fertilizer in commercial quantities without registration", contrary to the law.