Out of the 40 directors, 22, including chairperson Vaisahli Nagawade had earlier resigned from the board.
The state Dairy Development Department dissolved the board, which was under the scanner of Anti Corruption Bureau (ACB) and the Economic Offence wing over the alleged corruption.
The government has appointed Vishwas Patil, sitting managing director of the federation as the administrator.
"Since 22 members had resigned from their post, it was impossible to conduct the administrative business of the federation in the presence of 18 members. According to provision in cooperation law, 51 per cent members should be present to conduct the work. And hence, the remaining board of directors has been dissolved by the state government," Patil said.
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"We can continue with the administrator of any cooperative body for more than six months," he said.
Khadse had last week announced an inquiry of board of directors through ACB and EOW as cooperative department in its audit found misuse of government fund of more than Rs 100 crore. The inquiry will be conducted for a period of last ten years.
Former directors of Mahanand, including Deputy Chief Minister Ajit Pawar, former chairman of the federation and NCP leader Suresh Dhas, close confidante of NCP MP Supriya Sule and former chairman Vaishali Nagawade, are some of the high profile members, who will now face an inquiry by ACB and EOW.