The Bulgarian Football Union's (BFU) licensing commission said in a statement on Wednesday that CSKA, Lokomotiv Sofia and already-relegated Marek Dupnitsa and Haskovo have had their initial submissions rejected.
Those rejected have one week to appeal with CSKA and third-placed Lokomotiv stating they remained confident of being granted a licence.
Europa League hopefuls CSKA were league leaders before the two-and-a-half month winter break but have failed to score a goal in 10 successive games in 2015, picking up just four points in an 11-match winless run.
The Reds are now fifth in the standings.
In happier times, CSKA reached semi-finals in European competitions on three occasions between 1967 and 1989.
"I'm not surprised at all," Lokomotiv owner Nikolay Gigov told local media. "I know what we need to do in both directions - (to play in) Europe and Bulgaria.
"Our debt to the National Revenue Agency is about one million levs ($566.415). We have held talks with people from the agency and these conversations will be eventually resumed on Monday."
Many Bulgarian clubs face considerable infrastructure difficulties and are struggling to meet administrative, legal and financial conditions laid down by European soccer's governing body. (Reporting by Angel Krasimirov, editing by Pritha Sarkar)