The owner of Premier League club, Giwa FC, claimed he was enforcing a Jos court ruling that he should take over as NFF president.
However, police officers were called in to escort him out.
According to witnesses, Giwa was then driven away in his car with the police in tow.
It was unclear where he was taken as the police have so far declined to make that disclosure.
Giwa said he emerged president of the NFF in a controversial election on August 26, 2014, in Abuja.
Another election, which was endorsed by the world football governing body, FIFA, followed a month later in Warri, which then produced Amaju Pinnick as president of NFF.