"To put it bluntly, this story has been an unmitigated train wreck, and it seems every time management speaks to the Street, there is new negative incremental information forthcoming," said ISI Group analyst Brian Marshall.

HP said it has referred the alleged scam at Autonomy to the U.S. Securities and Exchange Commission's enforcement division and the UK's Serious Fraud Office for civil and criminal investigation. HP also said it would take legal action to recoup "what we can for our shareholders." However both the agencies declined to comment on this matter.

Whitman said that Autonomy’s investigation, both external and internal, will take multiple years as it will be fought in courts of both countries.

Whiteman defended the board's handling of the acquisition and blamed HP's auditors for failing to detect the problems.

"The board relied on audited financials, audited by Deloitte. Not Brand X accounting firm, but Deloitte," she said, adding that KPMG, another audit firm, was hired to audit Deloitte.

"Neither of them saw what we now see after someone came forward to point us in the right direction," Whitman said.

On Tuesday, a person familiar with the situation told Reuters that FBI was probing the HP-Autonomy allegations in concert with the Securities and Exchange Commission, although the inquiry was at an early stage. However both HP and Autonomy were not available to comment on the FBI probe and FBI too declined to comment.