FIFA does not tolerate government interference in football and in October it briefly suspended Nigeria following court action against directors of the federation.
"We are monitoring the situation (in Ghana)," FIFA said after Tuesday's police raid on the Ghana FA (GFA) in Accra.
The GFA said plain-clothed officers from the country's Economic and Organised Crime Unit (EOCU) removed nine computers and took the mobile phones of some staff in the raid.
"I believe that this is clearly an affront to the rule of law and without respect for good corporate governance," GFA spokesman Randy Abbey added.
The GFA said the seizure of documents had "stalled all administrative functions".
Two months ago the authorities requested information on all sponsorship contracts signed by the association, the GFA has said. The local governing body added it had sought extra time to gather the documents but had not received a response.
Ghana reached the World Cup quarter-finals, losing a penalty shootout to Uruguay, after being denied what would have been a winning goal at the end of extra time when opposing forward Luis Suarez handled the ball on the line.
Nigeria have twice upset FIFA in the last few months.
The country was nearly suspended shortly after the World Cup when President Goodluck Jonathan ordered the team's withdrawal from international soccer for the next two years in retribution for their first-round exit in South Africa.
He backed down under pressure from the world governing body.
In October, FIFA suspended Nigeria over political interference, which it said included court actions against Nigerian federation officials and the government's meddling in the national league.
The ban was lifted three days later after the court actions were dropped and the league was allowed to start.
The suspension of a country's FA means its national teams cannot play matches at any age level while its clubs are also banned from international competitions. Annual grants from FIFA are also cut off.