"These stale allegations are meritless and we reject them emphatically", Chris Morvillo of Clifford Chance and Reid Weingarten of Steptoe & Johnson said in a statement. HP has sought to blame Autonomy for its own crippling errors, and has falsely accused Mike Lynch to cover its own tracks.
The charge relates to Autonomy's US$11bn sale to computer behemoth Hewlett-Packard back in 2011 - a price that raised eyebrows in the City.
But now the DoJ has filed charges in a San Francisco court, accusing Lynch and other senior Autonomy executives of making false statement that inflated the value of the company.
The newspaper quoted lawyers for Lynch as saying the indictment was a "travesty of justice" and that he would contest the charges.
HP in 2012 took an $8.8bn write-down on the Autonomy acquisition, $5bn of which it said was due to Autonomy's "serious accounting improprieties, misrepresentation and disclosure failures" before its acquisition.
On a blogsite maintained by Dr Lynch on behalf of the former management team at Automony, he previously said HP's claim was "a desperate search for a scapegoat", and "one long disagreement over accounting treatments, and have nothing to do with fraud".
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They did this, according to the charge sheet, to hit their targets and thus guarantee their salaries, bonuses, and stock options, and to make Autonomy look attractive to purchasers - which it did, given that HP paid 11-figures for the company and its shares.
"It has no place in a U.S. court". Hussain is appealing the conviction and faces 20 years in prison if he fails.
The pair also said that the claims were related to a business dispute "over the application of United Kingdom accounting standards", and were central to a civil case against HP in English courts, "where it belongs".
HP has sued Lynch and Autonomy's former chief financial officer Sushovan Hussain for a reported $5 billion in damages.
"Mike Lynch is a world-leading entrepreneur who started from nothing and spent his life building a multi-billion dollar technology business that solved critical problems for companies and governments all around the world", the statement said. Hussain is now trying to overturn the conviction.