World governing body FIFA, who take a dim view of outside interference, have warned of suspension for the World Cup quarter-finalists.
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 in an inquiry into suspected tax breaches and fraud.
The GFA said the raid had brought it to an administrative standstill, prompting FIFA to warn government authorities to stop interfering.
In a letter to FIFA seen by Reuters, the government denied meddling.
"Their (crime office) investigations cannot be attributed to government and cannot be inferred to be government interference," sports minister Akua Sena Dansua wrote.
"Ongoing matters have nothing to do with central government and are purely matters being handled by a legally-established authority," he added in the letter.
Separately, EOCO issued a statement confirming it was investigating suspected tax breaches and fraud, and noted that it had tried earlier this week to return the seized material to the GFA on Wednesday but found that its offices were shut.
It confirmed the raid was connected to an investigation into the financial affairs of the GFA "which the Office has cause to believe have led to breaches of the laws of Ghana on tax, fraud and others".
On Wednesday, Ghana's clubs voted to pull their members out of the league, halting domestic football in the West African nation, the only African country to get past the group stage in this year's World Cup.
The GFA officially suspended the leagues on Friday.
"The Executive Committee of the Ghana Football Association has endorsed the decision of the GHALCA (Ghana League Clubs Association) to suspend all football related matters until further notice," it said in a statement.
"The Premier and Division One Leagues as well as FA Cup have been suspended. All national team assignments have also been put on hold."
FIFA, which briefly suspended Nigeria over political interference in the sport in October, has referred the matter to its emergency committee, which has the power to impose a suspension, if the situation does not change by Sunday.
