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 in the commercial city 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.
The Nigerian government dropped its corruption case against five officials of the football authority, including president Pinnick back in November.
But the EFCC and the country's Independent Corrupt Practices and Other Related Offences Commission (ICPC) still continues investigations into the NFF.
The latter seized properties belonging to top officials in September 2019 as part its probe, but is yet to bring a formal case against the federation or any of its member.
The NFF has previously blamed investigations by the anti-corruption authorities for the country's recent failures on the international scene.
Nigeria's under-17 and under-20s suffered round of 16 exits at last year's World Cup, the team of locally-based players failed to qualify for the 2020 African Nations Championship (CHAN) as well as suffering an early exit from the regional Wafu Cup tournament.
Despite being regarded as continental heavyweights, both the country's men and women's teams failed to qualify for the 2020 Tokyo Olympic Games football tournaments. // <\/s'+'cript>'); // --> //]]> From ICE
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