British officials covered up evidence that a Taliban commander killed by special forces in Helmand last year was in fact a Pakistani military officer, according to highly placed Afghan officials.

The commander, targeted in a compound in the Sangin valley, was one of six killed in the past year by SAS and SBS forces. When the British soldiers entered the compound they discovered a Pakistani military ID on the body.

It was the first physical evidence of covert Pakistani military operations against British forces in Afghanistan even though Islamabad insists it is a close ally in the war against terror.

Britain’s refusal to make the incident public led to a row with the Afghan president Hamid Karzai, who has long accused London of viewing Afghanistan through the eyes of Pakistani military intelligence, which is widely believed to have been helping the Taliban.

“He feels he has been telling everyone about Pakistan for the past six years and here was the evidence, yet London refused to release it, because they care more about their relations with Islamabad than Kabul,” said a source close to the president. “He knows Britain is worried about inflaming its large Pakistani population, but that is no excuse.”

So furious was Karzai that he threatened to expel British diplomats. When some months later he was informed by the governor of Helmand that British officials were secretly negotiating with the Taliban, he expelled two men and accused Britain of wanting to set up a training camp for former Taliban fighters.

Karzai will visit London next month for talks with Gordon Brown in an attempt to repair the strained relations between the two countries.

“He is very sad about the breakdown of relations with Britain,” said the source. “He loves British culture and poetry, had a British education [at a school in India], likes tea in the afternoon and thinks Gordon Brown is a very decent man, not a cheat.”

British officials in Kabul refused to comment on the allegation that they had covered up the discovery of a Pakistani soldier. They insisted Karzai’s government had been informed of the negotiations with the Taliban, adding that “the camp was just a place for them to be reintegrated, learn about hygiene and things”.

During the war against the Soviet Union in the 1980s, officers from Pakistani military intelligence regularly accompanied Afghan mujaheddin inside Afghanistan and directed operations.

The Afghan claims of Pakistani involvement in Helmand were backed by a senior United Nations official who said he had been told by his superiors to keep quiet after Pakistan’s ambassador to the UN apparently threatened to stop contributing forces to peacekeeping missions. Pakistan is the UN’s biggest supplier of peacekeeping troops.

The coalition’s refusal to confront Pakistan changed after the bombing of the Indian embassy in Kabul last July, when 41 people were killed. According to both British and US intelligence, phone intercepts led directly back to an Afghan cell of Pakistan’s military intelligence.

The past month has seen US forces carry out bombings and a ground raid on Pakistani territory. Claims of Pakistan’s involvement were rejected by Asif Durrani, the country’s chargé d’affaires in Kabul. “Afghanistan wants to blame someone else for its problems and Pakistan is just the whipping boy,” he said.

However, repeated accusations from Karzai about Pakistan’s active support for the Taliban have been backed by a senior US marine officer.

Lieutenant-Colonel Chris Nash, who commanded an embedded training team in eastern Afghanistan from June 2007 to March this year, told the Army Times that Pakistani forces flew repeated helicopter missions into Afghanistan to resupply a Taliban base camp during a fierce battle in June last year. Nash said: “We were on the receiving end of Pakistani military D-30 [a howitzer]. On numerous occasions Afghan border police checkpoints and observation posts were attacked by Pakistani military forces.”

Comments by Brigadier Mark Carleton-Smith in The Sunday Times last week that a decisive military victory against the Taliban was not possible and negotiations should be opened have received widespread backing.

General Jean-Louis Georgelin, France’s military chief, said: “There is no military solution to the Afghan crisis and I totally share this feeling.”

Robert Gates, the US defence secretary, who initially dismissed the brigadier’s comments as “defeatist”, said on Friday that the US was now prepared to back talks with the Taliban.

The deadly toll

— 120 British soldiers have been killed in Afghanistan since 2002

— At least 4,200 Afghans, including 1,450 civilians, have died this year alone

— Total cost of British operations in the Afghan war from 2001 to 2008 has been £3.2 billion

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