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.
"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."
FIFA added that the matter would be referred to its emergency committee, which could suspend the GFA, if the Sunday deadline was not met.
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