According to rules of the world’s football governing body, all leagues must conclude before the World Cup commences on June 14 and ends on July 15, or halt during the period.
However, following the rather late start of the Ghana Premier League last weekend, the GFA fears pulling the plug halfway will have more adverse effect on the already distorted football calendar.
"Fifa says that by June all leagues must end and this applies strictly to all countries, particularly those going to the World Cup, but we are not going," Nyantakyi told KweseESPN.
"We will negotiate with Fifa so we can slot matches in on days when there are no matches at the World Cup.
"It's important for us to synchronise our calendar with Europe because the clubs need it to be able to stay competitive, especially in the transfer market."
Against the expected 2017 kick-off date of the 2017-18 campaign, the league was scheduled to start in February this year due to the late conclusion of last season’s championship.
A court order, however, further pushed the commencement from February to March.
"I can't give you any assurance [that there will no anymore such cases] because I don't control those who are taking the GFA to court," Nyantakyi explained.
"We've had cases like this before which have been resolved. It's problematic.
"When I meet people from Fifa and tell them about clubs taking the federation to court, they marvel.
"The normal thing is to seek redress at the FA and the Court of Arbitration for Sports if you are not happy.
"Once a decision is made, we are duty bound to stick by that. We will never deviate.
"My appeal is that much as they have a right to seek legal action, these should go through the football processes."