The Istanbul club had asked on Friday to be allowed to play in the second-tier division, a day after the TFF rejected their appeal against their exclusion from this season's Champions League.
Any decision to relegate a club once the season had begun would mean it would be in a lower division in the following season, lengthening the punishment period.
"Fenerbahce expressed through its lawyers and the club's Vice Chairman in a meeting with the Federation on August 26 its demand to play in the Bank Asya first division, as well as in a statement on its website," the TFF said.
"However the club did not make a written request to the Federation.... also club officials and lawyers have stated there would be no such official written request... the TFF therefore decided there was no reason to change the decision it made on August 15," it said on its website.
Fenerbahce, who said their loss of revenue due to the Champions League exclusion would be some 25 million euros, have branded UEFA's stance on the issue as "unlawful", adding they were "innocent until proven guilty".
Among games reportedly under investigation are Fenerbahce's 4-3 victory over Sivasspor which clinched the title on the last day of the season and the cup final between Besiktas and IBB. Besiktas have returned the trophy pending the probe's outcome.
