The company's precarious position was revealed to investors after the firm recently uncovered "significant, and potentially fraudulent, accounting irregularities".
The popular bakery and continental cake shop opened a store in Chesterfield at the end of a year ago.
In its statement, the firm said that over the past 24 hours it had "undertaken further investigation into the financial status of the company".
Later on Wednesday, Patisserie Holdings said it had received a winding-up petition for its principal trading unit Stonebeach, with a hearing now scheduled for October 31.
Patisserie Holdings said on Wednesday that it was in communication with HMRC as it worked to "better understand the financial position of the group".
In addition, finance chief Chris Marsh has been suspended from his role and PwC has been drafted in to look through the company's books.
The crisis broke early yesterday morning when the company asked for trading in its shares to be suspended on the London Stock Exchange's junior AIM market and said it had unearthed potentially fraudulent accounting irregularities.
Entrepreneur Johnson bought a 70 per cent stake in the business in 2006, and still holds a 37 per cent interest, having enjoyed success with other chains like Pizza Express.
Johnson, Patisserie Holdings' executive chairman and biggest shareholder, said the business was "deeply concerned" about the developments.
According to Sky News, the hole in the company's accounts could be "over GBP20 million".
Patisserie Holdings - which had a market value of almost £450m before shares were suspended this week - operates from more than 200 stores.
In a separate statement a few hours later, the company said it had learned that Britain's HM Revenue & Customs (HMRC) had on September 14 filed a winding up petition against its main trading subsidiary, Stonebeach Limited, over 1.14 million pounds the tax office says it is owed.