Detectives investigating possible corporate charges against Rupert Murdoch's media empire have obtained evidence to suggest that News International paid private detectives to unlawfully access the phone records of a leading IRA mole who lives under the protection of the Ministry of Defence (MoD).

Senior Scotland Yard officers are analysing an invoice originally seized from a private investigator by the Metropolitan Police in 2007. The document – which dates from the time of the discredited original phone-hacking investigation – bills News International £850 for "Scappaticci phone records".

At the time the invoice was submitted, in April 2006, a senior News of the World executive had allegedly commissioned private detectives to find Freddie Scappaticci, Britain's top agent inside the IRA who was known by the codename "Stakeknife". David Cameron's former director of communications Andy Coulson was the newspaper's editor at the time. Last week, he was convicted of conspiracy to hack mobile phones.

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It is understood the explicit request to be paid for obtaining confidential phone records makes the invoice unique amongst the files held by the Metropolitan Police (Met) – and central to possible corporate charges. The request is effectively asking, in black-and-white, to be compensated for a criminal offence.

Given the sensitivities around Scappaticci, it is not clear why Scotland Yard failed to take any action against the News of the World or the private investigator when detectives seized the invoice in 2007. At the time, police chiefs were insisting criminality at the newspaper was confined to "one rogue reporter", Clive Goodman, who was jailed for phone-hacking in 2007.

The private investigator cannot be named for legal reasons, but, to clarify, he is not Glenn Mulcaire, convicted in 2007 in the original phone hacking trial. When The Independent on Sunday approached the unnamed investigator, he made the astonishing claim that the private phone records were obtained via a police source. Despite his involvement in the attempted compromise of one of the British Army's most sensitive assets, the private investigator said he was confident that he would not face any action.

"Nothing we have to worry about," he said. "If they are giving [us] stuff, they are giving [us] paperwork, who cares? That is their risk – nothing for us – nothing for us..." Later he added: "But if I was one of their bosses, I would sack 'em on the spot. 'You can't be trusted mate. Bye!'"

The private investigator, who has a criminal record, said the phone records belonged to Scappaticci's wife, who was thought to have stayed in Northern Ireland while her husband was in the witness protection scheme in the UK. The private detective said the News of the World was trying to track the Army informant's whereabouts "on the mainland". He said they managed to "turn round" a possible number to a phone box which they believed could be used by Scappaticci.

The IoS asked the private investigator whether he was worried he may have "committed any illegal acts by accessing that information from the police source then honing in on the landline number to the phone box". He replied: "Yeah, yeah. Not worried about that, not worried about that at all."

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Scotland Yard failed initially to take any action over the Scappaticci compromise. However, the Met has taken a much greater interest in its implications since August last year after a concerned third party emailed it to Commander Neil Basu, who has overall charge of the myriad investigations into News International.

The source was summoned to New Scotland Yard, London, where he was debriefed by Commander Basu, Detective Chief Superintendent Gordon Briggs and a senior Met lawyer. The invoice has also been emailed to Keith Vaz, chairman of the Home Affairs Committee.

Yesterday Mr Vaz said: "It is clear we have not reached the end of the revelations relating to hacking.

"The Prime Minister promised that on the conclusion of the criminal investigation into phone hacking a full investigation in to police involvement would be commenced. That time is drawing near and preparation for Leveson 2 must be started now. I will be writing to the PM to ask what steps he is proposing and what his timetable is for the next inquiry which he rightly promised."

Last week, Coulson was convicted of conspiracy to hack mobile phones. Five other News of the World journalists pleaded guilty to similar offences. After an eight-month trial that made headlines around the world, former News International chief executive Rebekah Brooks was acquitted of four charges.

However, the conviction of such a senior figure as Coulson has raised the possibility that News International – now rebranded News UK – could face a corporate charge, which may have serious consequences for the ability of the parent company News Corp to operate in the United States. The investigation into News UK as a "corporate suspect" caused pandemonium at the upper echelons of the Murdoch media empire when they learnt of the development two years ago.

Shortly after the company was informed it was under suspicion in May 2012, executives in the US ordered that the company dramatically scale back its co-operation with the Met. A News Corp analysis of the effects of a corporate charge, produced in New York, said the consequences could "kill the corporation, and 46,000 jobs would be in jeopardy".

Lawyers for the media giant pleaded with the Met and the Crown Prosecution Service not to prosecute the company, saying it would not be in the "public interest" to put thousands of jobs at risk.

Gerson Zweifach, group general counsel of News Corp, flew to London for emergency talks with the Met in 2012. According to Scotland Yard, he told police: "Crappy governance is not a crime. The US authorities' reaction would put the whole business at risk, as licences would be at risk."

The MoD has never confirmed or denied whether Scappaticci was "Stakeknife". He has always denied the claims. However, General Sir John Wilsey, a former commander of the British Army in Northern Ireland, was once secretly recorded describing Scappaticci as "our most important secret". "He was a golden egg, something that was very important to the Army," he said. "We were terribly cagey about Fred."

The MoD is mounting an unprecedented legal bid for secrecy in a High Court action against Scappaticci, who was said to be protected by the British state despite his suspected involvement in the deaths of dozens of loyalists, policemen and civilians. The ex-wife of another IRA informant is suing Freddie Scappaticci, along with the MoD and police, for alleged false imprisonment in 1994. The MoD and Police Service of Northern Ireland are seeking Closed Material Procedures, that would deny her lawyers access to material.

Paper trail

2003 Freddie Scappaticci widely reported to be the British Army's leading mole in the IRA's internal security unit known as the "Nutting Squad".

April 2006 A private investigator working for the News of the World sends invoice to News International for "Scappaticci phone records".

January 2007 Former NOTW royal editor Glenn Mulcaire jailed for phone-hacking.

February 2007 Met officers seize invoice in raid on private detective.

2006-2011 In the face of widespread evidence, Met maintains criminality at News of the World confined to "one rogue reporter" convicted of phone-hacking.

August 2013 "Scappaticci" invoice emailed to Commander Neil Basu.

June 2014 Former editor Andy Coulson found guilty of phone-hacking. Scotland Yard continues investigation into corporate offences at News International.