"These stale allegations are meritless and we reject them emphatically", they said, adding that "This case is unsupportable". Lynch, 18-cr-00577, U.S. District Court, Northern District of California (San Francisco).
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".
They said there was no conspiracy at Autonomy and no fraud against HP for the DoJ to take up. HP has sought to blame Autonomy for its own crippling errors, and has falsely accused Mike Lynch to cover its own tracks. "He has done nothing wrong and will vigorously defend the charges against him", it said.
The charges, filed in California on Thursday by USA prosecutors, add to the spaghetti-tangle of legal challenges that arose out of HP's ill-fated $11bn acquisition of Autonomy in 2011. HP has a long history of failed acquisitions.
The Serious Fraud Office in the United Kingdom halted a two-year investigation into HP's acquisition of Autonomy back in January 2015.
It comes as Sushovan Hussain, Autonomy's former chief financial officer, was convicted of fraud in a U.S. court earlier this year.
That is, artificially inflating revenues by backdating contracts, channel stuffing, and other forms of accounting fraud.
Allegedly, Mr Lynch made $815m from the fourteen charges.
The statement also claims Lynch is being made a scapegoat for HP's failures, framing the allegations as a business dispute over the application of United Kingdom accounting standards.
The Department of Justice said no court appearances had been scheduled yet and that both defendants "are presumed innocent until proven guilty beyond a reasonable doubt".
The company is seeking damages of $5bn from Lynch.
An investigation by the Serious Fraud Office into the sale of Autonomy has been brought to a close.
Lynch, who co-founded Autonomy in 1996 and was once dubbed Britain's answer to Bill Gates for turning the firm into a world leader, sold it to HP for $11billion (£7.1billion) in 2011. But within a year, HP claimed Autonomy had misrepresented its financial health.