Football Federation (TFF) chairman Mehmet Ali Aydınlar, who described the affair as Turkey's most serious soccer crisis before the proposal was voted down, voiced his frustration at the failure to reach an agreement.
Under the reform, which some clubs had proposed before the meeting, clubs believed to be involved in match-fixing would no longer face relegation but instead a minimum 12-point deduction.
"We have made all efforts so that Turkish football is not harmed or loses prestige abroad. But people spoke differently to us than they did behind their backs. Everyone is innocent and only we are guilty," Aydınlar said in an emotional final speech.
"We came with honour and that's how we'll go. History will write the truth," he added, saying the federation's management board would discuss the outcome of a meeting viewed as crucial to restoring the league's reputation and unity.
Pressure on the federation increased on Wednesday when UEFA general secretary Gianni Infantino said it must act quickly and take disciplinary action against those allegedly involved in the match-fixing, including some of the country's top clubs.
The scandal came to light last July when police detained 60 people in raids across Turkey, including Aziz Yildirim, the chairman of league champions Fenerbahçe. He remains in jail.
In December a Turkish court issued an indictment against 93 officials and players, including Yildirim and Olgun Peker, an ex-president of second division club Giresunspor.
They are both accused of being gang leaders among a raft of charges ranging from match-fixing to the payment of bribes.
Original media reports said some 19 first division matches were being investigated and the indictment refers to 13 matches.
"Turkish football is experiencing its most serious crisis, not just of today but since it was founded in 1923," Aydınlar told 240 delegates in the capital Ankara earlier in the day.
He had made a plea for unity but was faced with a barrage of fierce opposition to proposed changes in match-fixing sanctions.
BLACK STAIN
Strikingly, Fenerbahçe is among the clubs opposed to easing 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 "a black stain on the history of Turkish football".
UEFA insists however that the federation cannot wait and has not ruled out excluding clubs from future European competitions.
Galatasaray, which has not been named in the investigation, also opposes changing the regulations.
"As we have said before, you can't change the rules when the game is being played," Galatasaray chairman Unal Aysal said.
After the scandal broke, the TFF excluded Fenerbahçe from this season's Champions League, with runners-up Trabzonspor taking their place.
The first hearing in the court case is scheduled for Feb. 14. The indictment names eight clubs, including Fenerbahçe, Beşiktaş and Trabzonspor, who are currently in the Europa League. Fourteen players are among the defendants.
Controversy surrounding the match-fixing allegations was fuelled last month when parliament passed a law cutting prison sentences for match-rigging from a maximum 12 years to three.
The legal reform stirred rare dissent in Prime Minister Tayyip Erdoğan's ruling AK party but MPs defied a call by President Abdullah Gül to reconsider the reform.
He argued that it would mean the law no longer represented a sufficient deterrent and encouraged the view that it was passed to benefit certain individuals.
The court investigation has alleged manipulation in 19 matches, including Fenerbahce's 4-3 victory over Sivasspor which saw them clinch the league championship on the final day of last season when the allegations first surfaced.