Agents of the Serious Fraud Unit (SFU), who arrived at the Ghana Football Association with a court warrant, took away computers and mobile phones and prevented workers from entering the premises, they said.
"We have responded in writing to the unit and requested more time. However, there had not been any response," GFA president Kwesi Nyantakyi told journalists.
Last week, world football's governing body FIFA stated that the government could only order investigations into the distribution of money it gave to the association, but not funds from corporate bodies.
FIFA takes serious exception to government interference in football administration.
"The officers wanted to examine documents relating to sponsorship agreements between the GFA and various corporate bodies," GFA spokesman Randy Abbey said.
The government last month rescinded its move to impose former Ghanaian international Abedi Pele as a candidate for a vacant Confederation of African Football position when the GFA president had already applied for the job.
Ghana was the only African country to reach the quarter-finals of this year's World Cup held in South Africa.