The minister said, "The documentary exposes the gross malfunctioning of the Ghana Football Association (GFA), characterized by widespread fraud, corruption and bribery".
Before the last World Cup in Brazil in 2014, Nyantakyi was accused of signing a $170,000-deal for Ghana to play in a friendly organised by match fixers.
Minister for Youth and Sports Isaac Asiamah has disclosed that government has dissolved Ghana Football Association (GFA), following the premiering of Anas exposé to unravel rots in Ghana football.
"It stemmed out of the controversies generated by investigative report of Tiger Eye PI", he added.
According to Nyantakyi, he was deceived by the undercover journalists which he described as "scammers", he also apologised to President Akufo-Addo, Vice President Bawumia and the Ministers of state for associating them with the private conversations on the video.
FIFA responded earlier on Friday by banning Nyantakyi from "all football-related activity" for 90 days pending an investigation with a possible further suspension of up to 45 days.
"In the said report I committed a series of errors of indiscretion". I take sole and personal responsibility for the proceedings on the video.
Ghana, who have played at three previous World Cups, missed out on the this year's tournament which starts in Russian Federation on June 14.
"Government is shocked and outraged at the contents of the recently-aired video documentary, which captures the investigation conducted into football administration by the journalist, Anasa Aremeyaw, titled "Number 12': When Misconducted and Greed become the Norm", the statement read".
Nyanyakyi's resignation means the Ghana Football Association are now without a president and a vice president after George Afriyie was sacked from his post a month ago.
Nyantakyi, who is also a member of the Fifa Council, the world football body's legislative organ, was filmed in a hotel room allegedly taking a $65,000 bribe from a supposed businessman seeking to sponsor the Ghanaian football league.
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