US-Pakistan relations strained further after attack allegedly kills up to 28 and prompts ban on Nato trucks crossing Afghan border

An attack by Nato aircraft on Pakistani troops that allegedly killed as many as 28 soldiers and looks set to further poison relations between the US and Pakistan was an act of self-defence, a senior western official has claimed.

According to the Kabul-based official, a joint US-Afghan force operating in the mountainous Afghan frontier province of Kunar was the first to come under attack in the early hours of Saturday morning, forcing them to return fire.

The high death toll from an incident between two supposed allies suggests Nato helicopters and jets strafed Pakistani positions with heavy weapons.

The deadliest friendly fire incident since the start of the decade-long war also prompted Pakistan to ban Nato supply trucks from crossing into Afghanistan and to issue an order demanding the US quit the remote Shamsi airbase, from which the US has operated some unmanned drone aircraft. At border crossings, hundreds of supply trucks are reportedly stranded by the ban, with drivers fearing insurgents will take the opportunity to attack if they are not allowed to move.

Location of Nato air attack on Pakistani troops, and Shamsi airbase.

A spokesman for Nato's International Security Assistance Force (Isaf) said it was "highly likely" that aircraft which had been called into the area to provide "close air support" to troops on the ground was responsible for causing casualties among the Pakistani soldiers.

For their part, a statement by the Pakistani military claimed that it was they who were attacked first, forcing them to respond to Nato's "aggression with all available weapons".

According to Pakistani officials the 40 or so soldiers stationed at the outposts were asleep at the time of the attack. Government officials said the two border posts that were attacked had recently been established to try to stop insurgents who use bases in Afghanistan to attack Pakistan from crossing the border and launching attacks.

Afghan intelligence say the US-Afghan force was conducting operations against suspected Taliban training camps in the area.

The Obama administration promised a full investigation. Hillary Clinton, the US secretary of state, and Leon Panetta, the defence secretary, issued a joint statement saying they had each spoken to their Pakistani counterparts to express their condolences for the loss of life.

Pakistan was blunt that the killings represented a serious setback for the two countries' tattered alliance. The prime minister's office said the foreign minister, Hina Rabbani Khar, told Clinton on Sunday that the attack was unacceptable, showed complete disregard for human life and had sparked rage within Pakistan.

The vagueness of the border between Afghanistan and Pakistan is one potential, and relatively innocent, explanation for the incident. Drawn up by the British Raj in 1893, there is little agreement on where the so-called Durand Line actually falls, meaning troops from either side of the border can wander into the neighbouring country without realising it. One senior military official said that, in places, rival maps have discrepancies of "multiples of kilometres – sometimes as much as five kilometres".

Much of the fighting in Afghanistan is conducted by guerrillas based a short distance inside Pakistan. Nato forces are not allowed to cross the border and militants sometimes fire artillery and rockets across the line from locations close to Pakistani army posts.

And yet both sides have worked hard to try and minimise any confusion. The attack happened just a day after John Allen, the US commander of Nato forces in Afghanistan, met with Ashfaq Pervez Kayani, the Pakistani army chief, to discuss enhanced co-operation on the border.

But a more troubling explanation would be that insurgents in the area were operating under the nose of Pakistani security forces. Many Afghan officials believe Pakistan helps the Taliban with cross-border operations.

Edrees Momand of the Afghan Border Police said that a US-Afghan force in the area near the Pakistani outposts detained several militants on Saturday morning.

"I am not aware of the casualties on the other side of the border but those we have detained aren't Afghan Taliban," he said, implying they may have been Pakistani or other foreign national Taliban operating in Afghanistan.

Whatever the outcome of investigations, the incident is likely to do yet more damage to the critical relationship between the US and Pakistan. The alliance between the two countries has been repeatedly battered in the past year, first by the jailing of a CIA contractor and then by US special forces who raided deep inside Pakistani territory and killed Osama bin Laden.

More recently the US has accused Pakistan of backing a militant group who launched a 20-hour attack on the US embassy in Kabul.

Washington believes Pakistan continues to support the Taliban, a movement it publicly backed in the 1990s, in order to have influence in Afghanistan. But at the same time as supporting the enemies of the US, Pakistan remains crucial to the military mission in Afghanistan.

John Allen was quick to release a statement saying the incident had his "highest personal attention".

"My most sincere and personal heartfelt condolences go out to the families and loved ones of any members of Pakistan security forces who may have been killed or injured," he said.

Islamabad reacted with fury to the attack.

"This is an attack on Pakistan's sovereignty," said Pakistan's prime minister, Yousuf Raza Gilani. "We will not let any harm come to Pakistan's sovereignty and solidarity."

In a statement General Kayani promised "all necessary steps be undertaken for an effective response to this irresponsible act.

"A strong protest has been launched with Nato/Isaf in which it has been demanded that strong and urgent action be taken against those responsible for this aggression."

A cabinet committee convened by Gilani said the government would launch a complete review of its diplomatic, political, military and intelligence relationships with the US.

The vast bulk of Nato supplies arrive in Afghanistan by trucks that haul equipment up from the port of Karachi to the Khyber Pass, a key crossing point over the mountainous border into Afghanistan.

The shutting down of the border to Nato traffic has happened in the past during periods of Pakistani displeasure with Afghanistan and its foreign backers.

A similar incident last year in which two Pakistani troops were killed led to the closure of one of Nato's supply routes for ten days.

However, in recent years the alliance has opened up alternative supply routes through Central Asia, reducing its reliance on the route through Pakistan.