Ghana failed to make it past the group stage of the tournament and only picked up a single point from their three games against United States, Germany and Portugal.
This prompted the country’s president John Dramani Mahama to appoint a three-man commission to probe reports and allegations relating to the Black Stars' performance at the World Cup.
However, FIFA regulations state its "member associations have to manage their affairs independently and without influence of any third parties".
The Nigeria Football Federation (NFF) were overthrown by the country's government after their dismal campaign in Brazil, resulting in a FIFA ban, though the sanctions were lifted once the NFF were reinstated to independent power.
World football's governing body have already sent a letter, signed by deputy general secretary Markus Kattner, warning the country to stay out of the affairs of the Ghanaian Football Association and requesting the government to respect the autonomy of the federation or face possible sanctions.
Justice Senyo Dzamefe, the chairman of the commission, has hit back though, insisting FIFA cannot stop it from carrying out its duties, citing the sovereign independence of Ghana and the constitution that set up the commission.
Dzamefe said the commission would not be "intimidated" by FIFA, claiming they will only answer to Mahama.
The commission is currently adjourned until Wednesday after representatives of the Bank of Ghana failed to appear before it, even though officials of other state institutions were present.
The commission has the same powers of the High Court in Ghana and will examine matters such as the team's preparation for the World Cup and the government’s financing of the national team.
