The TFF said chairman Mehmet Ali Aydinlar had resigned and Husnu Gureli would stand in until a new federation election is held on February 27.
No reason was given for the resignations, but they came days after Turkish football clubs rejected a proposed regulatory reform designed to spare them from possible relegation over a match-fixing scandal in which several of the top clubs including champions Fenerbahce are implicated.
At last week's extraordinary general meeting of the federation, considered vital to restoring the league's reputation and unity, Aydinlar called the match-fixing affair the most serious crisis Turkish football had ever faced.
UEFA, European football's governing body, has called on Turkey to act quickly and take disciplinary action against those allegedly involved in the match-fixing.
Aydinlar, who became chairman only a few days before the match-fixing scandal broke, said in a statement that UEFA officials had made different remarks on the issue to the Court of Arbitration for Sport (CAS) and TFF, and he no longer had the patience to continue his work in an unethical environment.
A Turkish court issued an indictment in December against 93 officials and players, most notably Fenerbahce Chairman Aziz Yildirim, who is accused of being a gang leader among charges ranging from match-fixing to paying bribes.
Tuesday's announcement came one day after the federation said the chairman and his deputies would continue in their posts at the insistence of federation delegates "to prevent a worsening of the atmosphere of chaos in which football finds itself."
Turkish federation vice-president Goksel Gumusdag, among those who resigned on Tuesday, was detained over the match-fixing probe but later released.
MATCHES PROBED
When the investigation emerged after police raids last July, it was reported that 19 first division matches were being probed.
The indictment refers to 13 matches, including Fenerbahce's 4-3 victory over Sivasspor which saw them clinch the league championship on the final day of last season.
Under the proposed reform rejected last week, clubs believed to be involved in match-fixing would no longer face relegation, which is the current punishment, but would instead have faced a minimum 12-point deduction.
Despite being at the heart of the investigation, Fenerbahce led opposition among many clubs to the softening of punishments and said the federation must wait for completion of the legal process before acting.
In a written statement from his jail cell, Yildirim called the proposal to remove the threat of relegation "a black stain on the history of Turkish football."
UEFA has said, however, that the federation cannot wait and has not ruled out excluding clubs from future European competitions.
The Turkish federation excluded Fenerbahce from this season's Champions League, with runners-up Trabzonspor taking their place, in an initial move after the investigation started.
The first hearing in the court case is scheduled for February 14. The indictment names eight clubs, including Fenerbahce, Besiktas and Trabzonspor, who are currently in the Europa League. Fourteen players are among the defendants.
