"Having regard to the widespread nature of the apparent rot involving top GFA officials, NSA [National Sports Authority] officials, match commissioners, football administrators and referees, government has made a decision to take immediate steps to have the GFA dissolved", he said.
Mr Nyantakyi has not replied to multiple requests for comment while the GFA has said it would cooperate with any investigation.
The Ministry say they have been forced to act "as a result of the pervasive nature of the rot within the GFA" and that they have "taken immediate steps to have the GFA dissolved".
He said the government would soon announce provisional measures to govern football activities until a new association could be formed.
Youth and Sports Minister Isaac Asiamah told KweséESPN that the dissolution means all football activity is on hold in the country. He is considered the second most powerful person in Ghanaian football.
A police vehicle is pictured at the premises of Ghana Football Association in Accra.
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Despite releasing names of referees for this weekend's FA Cup matches, the Ghana Football Association (GFA) has backtracked, calling off all those matches - both men and women.
Asiamah said the decision had been a hard one to take, and is aware that it is likely to trigger some sort of action from world football's governing body FIFA, who strictly forbid the interference of government in the national federations.
In the apology which was contained in his resignation letter, Mr Nyantakyi also asked for forgiveness from Vice President Mahamudu Bawumia, Ministers and Deputy Ministers of State for his indiscretion in associating them with the private conversations in the Anas video.
He also received an undeserved $65,000 from the supposed businessman who was, in reality, an undercover journalist.
Nyantakyi's comes two days after Anas premiered his much talked about investigative piece on football corruption in Ghana.