CSKA will play in the amateur championship next season if it fails to merge with another first division club in time for the start of the Bulgarian league on July 20.
The Reds, as CSKA are known in the Balkan country, are in serious debt and last week coach Hristo Stoichkov said it had declared bankruptcy, although that had not been confirmed by club management or the BFU.
More than 1,000 supporters marched in downtown Sofia, blaming the national body for being too strict and for not allowing a merger.
Windows were smashed and some fans threw fireworks and sprayed graffiti near the main entrance of the BFU's building.
Former CSKA players and coaches including Stoycho Mladenov, who led the club to their last title in 2008, and former Bulgaria coach Plamen Markov also turned up at the protest.
They later condemned the violent scenes.
Local media reported that a security guard had hidden under a table and then began to beg the trouble-makers for mercy, and that a reporter who tried to take a photo during the attack was hit and his mobile phone broken.
"Police intervened immediately after receiving a call," the interior ministry said in a statement.
"It prevented more serious damage to the building. Police officers are working to identify and trace the offenders."
The BFU said in a statement that it was outraged at the "acts of vandalism".
"It's obvious that some people want to press the BFU to close its eyes at attempts at not observing the rules."
In an attempt to calm the escalating situation at the club, CSKA had earlier turned to former European Footballer of the Year Stoichkov, naming him coach.
Last Saturday, the club's owners said in a statement on the club's website that they had transferred their 6.5 million shares to Stoichkov, although the deal has yet to be concluded.
Stoichkov, frustrated by the actions of club management, didn't attend CSKA's last two training sessions this week, giving the owners a one-week ultimatum to finalise the transfer.
"I had two conditions, when I agreed to take over but they (the owners) didn't fulfil any," Stoichkov said.
"I want CSKA to be a club with transparent funding."
Earlier in the year CSKA chiefs fell out with die-hard supporters who accused them of incompetence and called on them to quit.
In September, angry CSKA fans set up a road blockade to protest against the owners and even asked the government for help.
During Saturday's protest the fans said they wanted their representatives to attend the share transfer.
"Next week, Hristo Stoichkov will receive CSKA's shares with zero debt and he'll become the owner of the club," Dimitar Borisov, one of CSKA's owners, told reporters earlier this week.
"I am not a lawyer, I can tell you anything more."
CSKA, the most successful Bulgarian club with 31 league titles, finished third last season, nine points behind champions Ludogorets.
Inept performances on the pitch have combined with controversy in the boardroom and stifling levels of debt have led to the current troubles.
It has led to insecurity in the dressing room, with more than half a dozen key players, including captain Ivan Bandalovski and Brazilian striker Michel Platini leaving the club earlier this week.
CSKA, who made three European semi-finals between 1967 and 1989, were barred from the 2008-09 Champions League after failing the meet licensing criteria, and their financial problems have led to them being denied a place in next season's Europa League.
- Sports & Recreation
- Hristo Stoichkov