Raymond Davis has been the subject of widespread speculation since he opened fire with a semi-automatic Glock pistol on the two men who had pulled up in front of his car at a red light on 25 January.
Pakistani authorities charged him with murder, but the Obama administration has insisted he is an "administrative and technical official" attached to its Lahore consulate and has diplomatic immunity.
Based on interviews in the US and Pakistan, the Guardian can confirm that the 36-year-old former special forces soldier is employed by the CIA. "It's beyond a shadow of a doubt," said a senior Pakistani intelligence official. The revelation may complicate American efforts to free Davis, who insists he was acting in self-defence against a pair of suspected robbers, who were both carrying guns.
Pakistani prosecutors accuse the spy of excessive force, saying he fired 10 shots and got out of his car to shoot one man twice in the back as he fled. The man's body was found 30 feet from his motorbike.
"It went way beyond what we define as self-defence. It was not commensurate with the threat," a senior police official involved in the case told the Guardian.
The Pakistani government is aware of Davis's CIA status yet has kept quiet in the face of immense American pressure to free him under the Vienna convention. Last week President Barack Obama described Davis as "our diplomat" and dispatched his chief diplomatic troubleshooter, Senator John Kerry, to Islamabad. Kerry returned home empty-handed.
Many Pakistanis are outraged at the idea of an armed American rampaging through their second-largest city. Analysts have warned of Egyptian-style protests if Davis is released. The government, fearful of a backlash, says it needs until 14 March to decide whether Davis enjoys immunity.
A third man was crushed by an American vehicle as it rushed to Davis's aid. Pakistani officials believe its occupants were CIA because they came from the house where Davis lived and were armed.
The US refused Pakistani demands to interrogate the two men and on Sunday a senior Pakistani intelligence official said they had left the country. "They have flown the coop, they are already in America," he said.
ABC News reported that the men had the same diplomatic visas as Davis. It is not unusual for US intelligence officers, like their counterparts round the world, to carry diplomatic passports.
The US has accused Pakistan of illegally detaining him and riding roughshod over international treaties. Angry politicians have proposed slashing Islamabad's $1.5bn (£900m) annual aid.
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But Washington's case is hobbled by its resounding silence on Davis's role. He served in the US special forces for 10 years before leaving in 2003 to become a security contractor. A senior Pakistani official said he believed Davis had worked with Xe, the firm formerly known as Blackwater.
Pakistani suspicions about Davis's role were stoked by the equipment police confiscated from his car: an unlicensed pistol, a long-range radio, a GPS device, an infrared torch and a camera with pictures of buildings around Lahore.
"This is not the work of a diplomat. He was doing espionage and surveillance activities," said the Punjab law minister, Rana Sanaullah, adding he had "confirmation" that Davis was a CIA employee.
A number of US media outlets learned about Davis's CIA role but have kept it under wraps at the request of the Obama administration. A Colorado television station, 9NEWS, made a connection after speaking to Davis's wife. She referred its inquiries to a number in Washington which turned out to be the CIA. The station removed the CIA reference from its website at the request of the US government.
Some reports, quoting Pakistani intelligence officials, have suggested that the men Davis killed, Faizan Haider, 21, and Muhammad Faheem, 19, were agents of Pakistan's Inter-Services Intelligence spy agency (ISI) and had orders to shadow Davis because he crossed a "red line".
A senior police official confirmed US claims that the men were petty thieves – investigators found stolen mobiles, foreign currency and weapons on them – but did not rule out an intelligence link.
A senior ISI official denied the dead men worked for the spy agency but admitted the CIA relationship had been damaged. "We are a sovereign country and if they want to work with us, they need to develop a trusting relationship on the basis of equality. Being arrogant and demanding is not the way to do it," he said.
Tensions between the spy agencies have been growing. The CIA Islamabad station chief was forced to leave in December after being named in a civil lawsuit. The ISI was angered when its chief, General Shuja Pasha, was named in a New York lawsuit related to the 2008 Mumbai attacks.
Although the two spy services co-operate in the CIA's drone campaign along the Afghan border, there has not been a drone strike since 23 January – the longest lull since June 2009. Experts are unsure whether both events are linked.
Davis awaits his fate in Kot Lakhpat jail in Lahore. Pakistani officials say they have taken exceptional measures to ensure his safety, including ringing the prison with paramilitary Punjab Rangers. The law minister, Sanaullah, said Davis was in a "high security zone" and was receiving food from visitors from the US consulate.
Sanaullah said 140 foreigners were in the facility, many on drug charges. Press reports have speculated that the authorities worry the US could try to spring Davis in a "Hollywood-style sting". "All measures for his security have been taken," said the ISI official. "He's as safe as can be."