FIFA have given Nyantakyi a 90-day ban from all football related activities with immediate effect.
His decision to step down follows an investigation by journalist Anas Aremeyaw Anas, who secretly filmed Mr. Nyankakyi discussing plans to set aside 25 per cent of a proposed sponsorship deal to a company he owns in a documentary called "When Greed and Corruption Become the Norm".More news: Whittaker favoured in non-title rematch with Romero for UFC 225
GFA's president Kwesi Nyantakyi was seen taking $65,000 in the documentary released on Wednesday.
"I wish to clarify that at no time prior to or subsequent to any deliberations on the video did I consult, contact or inform any government official about discussions on the video".
I wish to state my interest was to develop Ghana Football which led me to take the supposed investors to the President of the Ghana Football Association. Nyantakyi also has a role within FIFA's council, who are believed to be monitoring the situation.More news: US Special Forces attacked in Somalia by Al-Shabab
The Ghana Football Association issued a statement last month backing their president and saying he was innocent until proven guilty. However, parts of its rules is that governments should not interfere in football administration.
The information minister said the documentary "exposes gross malfunctioning of the Ghana Football Association characterised by widespread fraud, corruption and bribery".
Abdul-Hamid said interim measures would soon be announced. "The league is suspended until further notice as well as all activities and all programs of the Ghana Football Association". They will also drop out of the U20 World Cup.More news: Special counsel indicts Russian, adds charges against Manafort
Any FIFA ban could also affect the under-17 women's team, who are preparing for the U-17 World Cup; top club Aduana Stars, who are participating the CAF Confederation Cup; and the men's national team, who are due to play in three African Cup of Nations qualifiers later this year.