FIFA says it is aware that Ghana's government-mooted 2014 World Cup commission of enquiry has started its sittings and it is monitoring the situation.
Some media outlets had cast doubts over the a FIFA letter warning the government about the setting up of the commission but the world governing body says it is aware.
The world governing body last week expressed its opposition to some of the terms of reference of the commission insisting some violates its laws on the independence of the Ghana FA.
FIFA warned that transcending those boundaries could lead to a global ban on Ghana football which has sparked anxiety since the start of the commission's sitting on Monday.
The world governing body says government can investigate public funding for the team but looking into the management of the team is strictly within the reach of the GFA only.
FIFA says it is aware the commission has started its sitting and is it closely monitoring the situation in Accra.
"FIFA has acknowledged the setting-up of a Commission of Enquiry by the Ghanaian government," FIFA said in an emailed response to the media at the start of work by the commission.
"We are currently monitoring the situation and can’t make further comments for the time being nor speculate on the interpretation of articles 13 and 17."
Ghana risks an international ban if the country conducts a government-ordered Commission of Enquiry into its World Cup campaign.
And after the disastrous campaign in which more than US$3m had to be flown from Ghana to Brazil to pay the players - two of whom were later thrown out of camp for disciplinary reasons - Ghana President John Mahama called for a review.
However, Fifa prohibits governmental interference in the running of a national association.
And in its letter to the GFA, dated 7 August, it added: "Should any decision be rendered by the Commission against GFA officials thereby removing them from office, it would be considered as interference in the GFA affairs and the case would be brought to Fifa's highest instances for appropriate sanctions."
In the past, such sanctions have involved international suspensions from all forms of football for governmental interference - with Fifa in no doubt as to how that may be developing in Ghana.