Fifa has warned the Ghana government that future interference in the administration of the game in the country could lead to sanctions.
The governing body is disappointed that Ghana football, which is seen by many as a good example for other countries, is reeling under government pressure.
Fifa made these conclusions after investigating claims of intrusion.
Under Fifa rules, national football associations must not be subject to government control.
But the Ghana Football Association (GFA) has recently come under intense pressure from government over various issues.
The government withdrew its order to impose Abedi Pele as a candidate for a vacant Caf post after the GFA rejected the request two weeks ago.
Even though Fifa is pleased that sanity has been restored, the governing body warns that future attempts could have serious consequences.
"We appreciate the fact that the government has now realized that it was not competent to nominate candidates for elective functions within the football organisation structure," Fifa general secretary Jerome Valcke wrote in letter seen by the BBC.
"However we would like to draw the attention of the government to the fact that the GFA must manage its affairs independently with no influence from third parties at stated in Fifa statutes.
"Violations of such provisions might lead to sanctions as stated in Fifa Statues Article 17.13."
Ghana football has soared over the past few years under Kwesi Nyantakyi's reign culminating in two successful World Cup appearances in 2006 and 2010.
The Black Satellites gained rave reviews last year after it became the first African side to win the U20 World Cup in Egypt.
Fifa fears that attempts by government elements to interfere in the administration of the sport in the country could undermine Ghana progress in world football.