The Reds, who are Bulgaria's most successful club with 31 league titles, were barred from the Champions League in 2008-09 after failing to meet the licensing criteria.
"CSKA are currently supervised by UEFA, just like (Serbia's) Red Star Belgrade," the BFU's Borislav Mihaylov, who is also a UEFA Executive Committee member, told reporters.
"UEFA representatives will conduct an audit of the club later in September and if they find something wrong, CSKA will lose their licence with immediate effect."
CSKA were knocked out of this season's Europa League in July. Mihaylov warned the club could be excluded from Europe for up to three years.
"I hope everything will be OK despite the problems," Mihaylov, a former Bulgaria keeper capped 102 times by his country, said. "They're a club with a lot of supporters and big traditions."
CSKA owe transfer sums to clubs and players as well as money to the state and creditors, estimated by local media to be almost 80 million levs (£32.4 million).
In July, CSKA were handed a transfer ban until Aug. 31 by the BFU over the signing of the Madagascar international Anicet from Chernomorets Burgas.
CSKA reached semi-finals in Europe three times between 1967 and 1989 but have struggled to revive their success in recent years and have not won the domestic title since 2008.
The Reds are eighth in the domestic league with five points from four matches, seven points behind champions Ludogorets and city rivals Levski.