The charges allege that between 2009 and 2011, Dr Lynch and former Autonomy finance executive Stephen Chamberlain issued statements which artificially inflated the company's performance between 2009 and 2011 - a claim he has always denied.
However, in a statement provided to The Register, Lynch's lawyers called the indictment "a travesty of justice".
Lawyers for Lynch said the charges amount to a business dispute over the application of United Kingdom accounting standards. Lynch, 18-cr-00577, U.S. District Court, Northern District of California (San Francisco).
"HP has sought to blame Autonomy for its own crippling errors, and has falsely accused Mike Lynch to cover its own tracks", said Lynch's lawyers, Chris Morvillo of Clifford Chance and Reid Weingarten of Steptoe & Johnson.
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".
While the results for HP in the fourth quarter were rosy, the company is still counting the costs from the fall-out of Hewlett-Packard's ill-fated acquisition of United Kingdom tech firm Autonomy, the software giant founded by Irish-born entrepreneur Mike Lynch. HP has a long history of failed acquisitions.
"Mike Lynch will not be a scapegoat for their failures". A Serious Fraud Office investigation in the United Kingdom was closed in 2015 without charge, but since then we've seen suit and countersuit leading up to this moment.
Prosecutors have gone afterLynch after his former finance chief, Sushovan Hussain, was found guilty in April of accounting fraud.
Allegedly, Mr Lynch made $815m from the fourteen charges.
Lynch's lawyers told the Financial Times that the charges were a "travesty of justice" and that the proper venue for the case is the courts of England where HPE is pursuing a civil case against Lynch "over the application of United Kingdom accounting standards". "He has done nothing wrong and will vigorously defend the charges against him". But within a year, HP claimed Autonomy had misrepresented its financial health.
Lynch was also an early investor in UK-based cybersecurity unicorn Darktrace.
For its fourth quarter, Hewlett-Packard records a charge of $8.8 billion in its software unit, which had "serious accounting improprieties.and outright misrepresentations" when HP bought it.