"It's obvious that the referees committed striking errors that affected the results of some matches," BFU president Borislav Mihaylov told a news conference on Monday.
Several clubs have criticised refereeing this season, and champions Levski Sofia called for the resignation of Mihaylov and referees' chief Dimo Momirov last month.
Hundreds of Levski fans gathered in downtown Sofia to protest against the BFU and the referees following their team's 4-1 loss to Cherno More Varna in the Bulgarian Cup on Sunday, accusing official Stanislav Stavrov of "crime against football".
Mihaylov announced that Stavrov and Alexander Kostadinov, who took charge at CSKA Sofia's 1-0 win over Litex Lovech in the domestic cup on Saturday, had been taken off the referees' list for an unspecified period.
In September 2008, Bulgarian referees voted unanimously to appoint former international match official Momirov as the referee commission's chairman following the dismissal of the seven-member body.
Mihaylov, however, said that Momirov and the commission had failed to cope with their duties.
"They've had enough time to solve the problems in Bulgarian refereeing and they were given full control in the appointment of officials but you see that it didn't work out," said Mihaylov.
Commission deputy chairman Kostadin Gerginov said: "The referees made mistakes but I think it's important to say that they didn't commit them intentionally. Errors are part of the game all around the world, not only in Bulgaria."
The BFU said they would appoint a new commission chief in January.
