Levski also called for the resignation of BFU president Borislav Mihaylov and referee commission chief Dimo Momirov.
"We insist the BFU holds an extraordinary congress and we appeal to the whole football public to demand it since the domestic championship is pre-determined," Levski said in a statement on Thursday.
"The management of Levski expresses its indignation at the attempt of the Bulgarian championship to be decided by no footballing instruments," added the club.
The BFU issued a statement rejecting Levski's accusations.
"We accept Levski's statement as a thoughtless attempt to manipulate the millions of club fans... as there's an accumulated strain following the recent lack of success on and off the field," the BFU said on its website.
"Instead of seeing their own managerial failure, Levski prefer to write declarations to transfer the responsibility to the most convenient target -- the BFU.
"The BFU, however, refuse to be a target and will continue to do its best to facilitate the work of professional clubs."
Several Levski officials accused referee Nikolay Yordanov of bias after an ill-tempered 2-2 draw against Litex which left them eight points adrift of the leaders after 13 matches.
Three players, two from Levski, were sent off and Levski coach Georgi Ivanov was also dismissed during the match.
"We were deprived of the win in a key match by biased refereeing," said Levski's senior official Georgi Markov.
"That's why Nikolay Yordanov and Dimo Momirov are persona non grata at our stadium from now on. We insist the BFU suspend them from football for life."
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