"I'm fed up, I'm leaving," the former Barcelona striker said in a letter addressed to local media.
"I agreed to start coaching without a contract and I had a great desire to help.
"I had the support of the players and my staff. We endured until it became clear there's no chance of promises being fulfilled," added Stoichkov, who did not attend CSKA's training sessions for the last 10 days.
CSKA are the most successful Bulgarian club with 31 league titles but have hit difficult times of late with inept performances on the pitch combining with controversy in the boardroom and stifling levels of debt.
Titan Sport, a subsidiary of Titan International Holdings, have overseen the tricky times since acquiring 100 percent of CSKA shares in 2009.
In an attempt to calm the escalating situation ahead of the start of the new season on July 20, they turned to crowd favourite Stoichkov last month for their fourth coach of the year.
Stoichkov, who won three league titles and four national cups as a CSKA player in the 1980s, received a rapturous welcome as thousands of fans cheered him and let off flares during the club's first pre-season training session.
But the problems quickly followed.
Only two weeks later, the owners said in a surprise statement on the club's website that they had transferred all their 6.5 million shares to the 47-year-old Stoichkov, although the deal has yet to be concluded.
Stoichkov also said that several businessmen were ready to start financing the Reds but the owners had prevented the change of the ownership.
"It is not my understanding of fair, transparent and professional work," said Stoichkov. "This is no way to achieve high goals if there's no respect between players, coaches and officials on the one hand, and the club owners on the other.
"Lies cannot be endless and we cannot go forward. Or at least I cannot do so."
CSKA, who made three European semi-finals between 1967 and 1989, finished third in the league last season, nine points behind champions Ludogorets.
The off-field problems have 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 in the last two weeks.
Only a small number of CSKA players continue training over mounting uncertainty ahead of the start of the new season.