The investigation by the Economic and Financial Crimes Commission (EFCC) is looking at wide-ranging fraud allegations over how money meant for football sponsorship and development cannot be properly accounted for, according to the agency.
Akinwunmi, head of Lagos state football's governing body, confirmed he was questioned and was released from custody without any charge.
"I was indeed questioned as were/are numerous others as part of their wide ranging investigations," Akinwunmi, who has always denied any wrongdoing, told BBC Sport on Saturday.
Investigations into alleged corruption have been conducted for the past three years and other top NFF officials have been interviewed. They have always denied any wrongdoing.
The NFF has been under scrutiny both on and off the pitch in recent months.