The British software company has been accused of lying about its finances and boosting figures through various accounting tricks to convince HP to buy Autonomy, which it did for $9.7bn (£7.1bn) in October 2011.
But founder and ex-chief executive of Autonomy Mike Lynch, who made £500m from the deal, "flatly refutes" the claims by HP, which came as HP announced a write-down of $8.8bn (£5.5bn) relating to the purchase of the Cambridge (BSE: CTE.BO - news) -base firm.
Mr Lynch told Sky's Jeff Randall the write-down was a result of mismanagement and a destruction of Autonomy's value as a result.
He said: "This is a company that is in utter chaos. Yesterday it delivered its worst results in probably 70 years.
"But I'm not going to be HP's scapegoat for the fact that the company is in utter disarray."
The Silicon Valley computing firm is struggling to reinvent itself as PC and printer sales shrink.
Mr Lynch added that its auditors Deloitte had gone on record to say there were no problems with the company's books. He added that HP's due diligence review was extensive at the time of the takeover - involving KPMG, Barclays (LSE: BARC.L - news) and Perella Weinberg.
Mr Lynch said there was a degeneration of the business after a change of leadership, with hundreds of people leaving Autonomy as well as the senior management. Mr Lynch left nine months after the deal.
He said: "Leo Apotheker who did the deal saw the vision of taking Autonomy and doing a big software business in HP.
"The problem was that they were ousted in a coup d'état and suddenly we are a situation where we no longer fitted the flip-flopping strategy."
An internal investigation into Autonomy's finances was launched by HP after it said a whistle-blower came forward alleging suspect accounting and business practices.
Once HP bought the company, Autonomy's reported revenue growth and profit margin quickly declined.
HP CEO Meg Whitman said the company had been booking the sale of computers as software revenue and claiming the cost of making the machines as a marketing expense. Revenue from long-term contracts was booked up front, instead of over time.
The case has been referred to the US Securities and Exchange Commission and the UK's Serious Fraud Office (SFO), Ms Whitman said. The FBI is also said to be investigating the claim.
Contacted by Sky News, both the FBI and SFO declined to confirm any investigations had been launched.
The company will also try to recoup some of the cash it paid for Autonomy through lawsuits.
Mr Lynch said he was surprised that he had not been contacted by HP.
He said: "They want to create a lot of PR noise here without having a situation where we can actually answer it."
Autonomy makes search engines that help companies find vital information stored across computer networks.
:: A spokesperson for HP was unavailable for comment on the claims made by Mr Lynch.