The former finance director of British software group Autonomy has been accused by US prosecutors of “intimidating, pressuring, and paying off” individuals who questioned his company’s financial practices.

In a 12-page indictment, filed on Thursday and seen by the Guardian, Sushovan Hussain is alleged to have masterminded an elaborate financial fraud designed to deceive investors, analysts, regulators, and auditors.

Following a four-year investigation by the US Department of Justice, the British company director is facing a criminal trial in San Francisco. If found guilty, he could serve up to 20 years in prison and a be forced to pay multimillion-dollar penalty.

Hewlett-Packard (HP), the Californian computing group, paid $11bn (£8.7bn) to buy Autonomy five years ago, the biggest ever takeover of a European technology group. Mike Lynch, the Autonomy founder, collected over £517m for his shares, while Hussain received £10m. HP now claims it overpaid because Autonomy’s directors exaggerated the company’s value.

Lynch, who holds an OBE and advises the British government as a member of its council for science and technology, has not been charged. Sources said this weekend that prosecutors may be hoping to pressure Hussain into turning against his former boss and providing evidence with which to prosecute Lynch. However, an alternative source familiar with the legal process questioned this hypothesis, saying the statute of limitation would now have passed and action against Lynch could no longer be taken.

Hussain is squaring up for a full-scale legal battle. He has retained John Keker, the elite US attorney who defended banned cyclist Lance Armstrong during the justice department’s investigation into doping by professional cyclists. He is best known for successfully prosecuting White House aide Oliver North over the Iran-contra affair.

A Vietnam veteran and marine corps leader who went on to become one of America’s most formidable lawyers, Keker’s other clients have included the Black Panther party leader Eldridge Cleaver and Frank Quattrone, an investment banker who overturned three trials before being exonerated over allegations linked to the stock market listing of companies during the dotcom bubble.

Keker said in an emailed statement that his client would be “acquitted at trial”. He said Hussain was innocent of wrongdoing, had defrauded no one, and had acted at all times “with the highest standards of honesty, integrity and competence”.

“It is a shame that the Department of Justice is lending its support to HP’s attempts to blame others for its own catastrophic failings,” Keker said in the email. “Mr Hussain is a UK citizen who properly applied UK accounting rules for a UK company. This issue does not belong in a US criminal court.”

In one of the more serious claims, the indictment alleges that on 28 July 2010, Hussain “caused Autonomy to fire a finance officer in the United States who questioned whether Autonomy’s financial statements were accurately stated”.

Prosecutors have not named the individual concerned. However, in a case brought by HP against Lynch and Hussain in London’s high court last year, the employee is identified as Brent Hogenson, Autonomy’s chief financial officer in the US until his dismissal on 28 July 2010.

From October 2009, prosecutors allege that Hussain, together with others, “engaged in a fraudulent scheme to deceive” investors in Autonomy.

The objective was to ensure Autonomy exceeded the quarterly projections for its revenue and profit growth, “to maintain and increase the defendant’s position within the company, to enrich themselves and others through bonuses, salaries and options”, and to make Autonomy more attractive to potential purchasers and HP.

A long list of charges claims the ex-finance director misled market analysts, made false entries in company accounts, and made “false and misleading statements to Autonomy’s regulators in response to inquiries about its financial statements”.

Hussain is also accused of “intimidating, pressuring, and paying off persons who raised complaints about or openly criticised Autonomy’s financial practices and performance”.

Similar claims against Hussain and Lynch were made by HP last year. The US firm, which acquired Autonomy in a doomed attempt to transform itself from a manufacturer of personal computers and printers into a more profitable software company, is suing the pair at the high court in London.

HP is claiming $5.1bn in damages in what is believed to be the largest ever civil prosecution against British nationals. Its suit claims Hogenson, Autonomy’s US finance chief, was dismissed after raising concerns with the firm’s auditor, Deloitte, and with the then UK regulator, the Financial Services Authority (FSA).

Hogenson sent an email to the FSA on 26 July 2010, allegedly raising a red flag over Autonomy’s dealings with resellers of its software. Autonomy was once a leading light in “Silicon Fen”, the cluster of tech firms around Cambridge university. It specialised in corporate search software, designed to speed up the process of trawling through massive databases of text and audio files.

Lynch is counter-suing HP for $160m, claiming the firm has ruined his reputation. Neither of the British cases is expected to go to trial before 2018.

Despite claims that Hogenson attempted to blow the whistle, British regulators did not open a major investigation until February 2013, after HP had made its first complaint about accounting improprieties at Autonomy. The Serious Fraud Office, which led the investigation, dropped the case in January 2015, citing “insufficient evidence for a realistic prospect of a conviction”.

Lynch has placed his earnings from Autonomy into a new venture, Invoke Capital, which invests in start-up tech firms. He joined George Osborne on a trade mission to China in 2013, and is due to speak at a conference organised by the website TechCrunch in London in December.