In a statement carried on the GFA website, Nyantakyi apologised "unreservedly" for "a series of errors of indiscretion" after Federation Internationale de Football Association launched an ethics investigation into his activities.
Mr Nyantakyi has not replied to multiple requests for comment while the GFA has said it would cooperate with any investigation.
The two-hour documentary, "When Greed and Corruption Become the Norm", is the work of undercover journalist Anas Aremeyaw Anas and Wednesday's public viewing was the first since it was released to the authorities last month.
The scandal has indicted 66 Ghanaian referees as well as 14 FA officials in taking bribes, with the FA president Kwesi Nyantakyi finding himself in the midst of the allegations.
My decision is as a result of deliberations I have had with family and my associates.
Government on Thursday indicated its resolve to dissolve GFA in a bid to sanitise football administration.
Abdul-Hamid said the government was "shocked and outraged" at the claims, which included referees apparently accepting bribes of at least $100 to throw matches.
The information minister said the documentary "exposes gross malfunctioning of the Ghana Football Association characterised by widespread fraud, corruption and bribery".
"Consequently, the police are to take all such relevant measures as are necessary to ensure that the contents of the documentary are rapidly and thoroughly investigated; having regard to the widespread nature of the apparent rot involving top GFA officials, top NSA officials, match commissioners, football administrators and referees, government has chose to take immediate steps to have the GFA dissolved".
Abdul-Hamid said interim measures would soon be announced. They will also drop out of the U20 World Cup.
Football is by far the most popular sport in Ghana and while the national team, the Black Stars, failed to reach this year's World Cup finals, they were quarter-finalists in South Africa in 2010.
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