FIFA, which briefly suspended Nigeria over political interference in the sport in October, warned Ghana that continued action would have "adverse consequences" after the GFA's offices were raided on Tuesday.
"FIFA hopes that the Ghanaian authorities will reconsider their actions and thus avoid the deepening of a crisis which will only bring adverse consequences for the football lovers in Ghana," said FIFA in a statement sent to Reuters.
Football's governing body added that the matter would be referred to its emergency committee, which has the power to impose a suspension, if the situation did not change by Sunday.
The row erupted on Tuesday when plain-clothed officers from the country's Economic and Organised Crime Unit (EOCU) raided the GFA headquarters and removed nine computers and took the mobile phones of some staff.
The GFA said this had brought it to an administrative standstill.
"FIFA recognises that the Ghanaian government audits the GFA accounts, but only related to the attribution of public funds," said FIFA's statement. "This excludes funds coming from other sources, such as FIFA or CAF (the Confederation of African Football).
"However, due to the EOCU move, the GFA had to stop all its activities, including the running of the league or other development programs.
"For FIFA it is not acceptable if the GFA is not in a position anymore to exercise the core of its mandate, which is to run football in the country, because of government intervention."
On Wednesday, the Ghanaian clubs voted to pull their members out of the league, bringing domestic football in the West African nation to a standstill.
The GFA has not given reasons for the raid but noted authorities had two months ago requested information on all sponsorship contracts signed by the GFA.
It added that it had sought extra time to gather the documents but had not received a response.
Ghana's World Cup success means it may now experience the same problems as other African football nations such as Cameroon or Nigeria, with the arrival of private sponsors creating friction with the government.
Suspension would mean that the national team would be grounded and that the country's clubs would also be unable to take part in international competitions.
