It says there is an unexplained $1m (Â£640,000) hole in the Ghana Football Association's (GFA) finances.
The GFA denies the allegations, saying there was no corruption ahead of the 2014 Brazil World Cup.
The government had to send $3m in cash by plane to players in Brazil to avert a final-game boycott over bonuses.
GFA spokesman Ibrahim Saanie Daara told Joy FM that it was still waiting to receive a copy of the full report, but would cooperate with any future investigations.
The report also calls for an investigation into a $200,000 payment made to GFA chief Kwesi Nyantakyi for a friendly match in the lead-up to the 2014 World Cup.
Mr Nyantakyi has not yet responded to the report.
A government-backed commission of inquiry was set up to examine the failures surrounding Ghana's World Cup campaign, which was seen as a national embarrassment at the time.
The report released by the presidency on Friday sets out the government's response to the inquiry.
The Black Stars failed to win a single game at the 2014 tournament, and two of their key players were sent home for alleged indiscipline.
Ghana's government has called for a "forensic audit" of the country's football body over allegations of missing World Cup campaign funds.