The Ghana government has until Sunday to steer clear from the affairs of the Ghana Football Association (GFA) or the country will face "adverse consequences", Fifa has warned.
The world governing body has referred the stand-off in Ghana to its emergency committee which will rule on Ghana by Sunday.
Fifa's previous 'adverse consequences' warning have led to international bans on countries in the past.
This means if the government agencies fail to stop the raids and threats on the GFA, Ghana will be banned from international football.
The world governing body was reacting to a raid carried out by the country's anti-graft agency on the GFA's offices on Tuesday.
Fifa's warning came after plain-clothed officers from the country's Economic and Organised Crime Unit (EOCU) raided the GFA headquarters on Tuesday and removed nine computers and took the mobile phones of some staff.
Fifa laws prevent governments from seeking to control the federations in their countries which have led to the warning.
"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," FIFA said in a statement sent to Reuters.
"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."
The GFA said the subsequent removal of computers and mobile phones had brought it to an administrative standstill and on Tuesday, it suspended all football-related activities until further notice.
Meanwhile, Fifa - which takes a dim view of third-party interference in the running of a FA - has sent a second warning to Ghanaian authorities.
"Fifa recognises that the Ghanaian government audits the GFA accounts, but only related to the attribution of public funds," said Fifa in its statement.
"This excludes funds coming from other sources, such as Fifa or Caf (the Confederation of African Football).
"However, due to the (EOCO) move, the GFA had to stop all its activities, including the running of the league or other development programmes.
"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, 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.
The raid on the GFA came just two weeks after the federation snubbed a government request to put Abedi Pele forward as Ghana's candidate for a Caf executive committee position.
There have been several attempts by elements in government to seek to control the GFA including in the appointment of a new Black Stars coach, and seeking people on the various committees on the GFA.
Fifa added that the matter would be referred to its emergency committee, which could suspend the GFA, if the Sunday deadline was not met.