HP acquired Autonomy in 2011.
Autonomy founder Mike Lynch said HP took over his firm in a $11bn deal, despite being warned of accounting practices.
HP acquired the UK-based Autonomy in 2011 and was forced to book an $8.8bn writedown on the company just a year later.
The company is suing Lynch and Autonomy’s former finance director Sushovan Hussain for damages of around $5.1bn over allegations of fraud.
Lynch said concerns like the sale of hardware and the recognition of revenues in agreements with resellers, were raised in a due diligence report by KPMG.
The report also reveals that KPMG told HP the difference between European and US accounting standards could affect historical growth rates for the firm.
Lynch told Reuters, "The KPMG report directly contradicts the statements HP made about Autonomy on which its whole case is based.
"HP said it did not know things that it plainly did."
A HP spokeswoman has however said, "HP had no knowledge of Lynch and Hussain’s contrived sales to value added resellers and other improper transactions and accounting practices, all of which artificially inflated Autonomy’s reported revenues, misrepresented its rate of organic growth and overstated its gross and net profits."
The report also said that HP’s then chairman Ray Lane tried to stop the deal.
Earlier this year, Lynch sued HP over allegations that he mismanaged Autonomy that was sold to HP in 2011.