Lawyers for Lynch told the Financial Times the indictment was a "travesty of justice", since it brought to a criminal court a "business dispute" over the application of United Kingdom accounting standards overseas.
Mike Lynch will fight the charges.
"It has no place in a United States court".
His lawyers added that HP had sought to "blame Autonomy for its own crippling errors" as well as "falsely accused Mike Lynch to cover its own tracks". "The claims amount to a business dispute over the application of United Kingdom accounting standards, which is the subject of a civil case with HP in the courts of England, where it belongs".
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The BBC has obtained a statement from his lawyers, Chris Morvillo of Clifford Chance and Reid Weingarten of Steptoe & Johnson, which describes the indictment as "a travesty of justice".
Mike Lynch picture in 2010. HP later paid investors $100m for the botched acquisition.
The Serious Fraud Office in the United Kingdom halted a two-year investigation into HP's acquisition of Autonomy back in January 2015.
Earlier this year, the Financial Reporting Council began disciplinary proceedings against former bosses at Autonomy and auditors at Deloitte linked to the alleged fraud at the software firm. "He has done nothing wrong and will vigorously defend the charges against him", it said. In 2011, the company was bought by HP for $11 billion in a move that was supposed to form the central part of the USA group's move into software.
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".
They and former Autonomy chief financial officer Sushovan Hussain are accused of using "false and misleading financial statements" between 2009 and 2011 to make Autonomy more attractive to a potential purchaser. It is seeking $5 billion in damages against Lynch and Hussein in a civil lawsuit filed in the United Kingdom.