A secret order issued by George Bush giving US special forces carte blanche to mount counter-terrorist operations inside Pakistani territory raised fears last night that escalating conflict was spreading from Afghanistan to Pakistan and could ignite a region-wide war.

The unprecedented executive order, signed by Bush in July after an intense internal administration debate, comes amid western concern that the war against the Taliban in Afghanistan and its al-Qaida backers based in "safe havens" in western Pakistan's tribal belt is being lost.

Following Bush's decision, US navy Seals commandos, backed by attack helicopters, launched a ground raid into Pakistan last week which the US claimed killed about two dozen insurgents. Pakistani officials condemned the raid as illegal and said most of the dead were civilians. US and Nato commanders are anxious to halt infiltration across the Afghanistan-Pakistan border of insurgents and weapons blamed for casualties among coalition troops. The killing of a US soldier in eastern Afghanistan yesterday brought American losses in 2008 to 112, the deadliest year since the 2001 intervention. The move is regarded as unprecedented in terms of sending troops into a friendly, allied country.

But another American objective is the capture of Osama bin Laden, the al-Qaida leader held responsible for organising the 9/11 attacks. He and his second-in-command, Ayman al-Zawahiri, are thought to be hiding in the tribal areas of north and south Waziristan.

Bush's decision to extend the war into Pakistan, and his apparent hope of British backing, formed the background to a video conference call with Gordon Brown yesterday. "What's happening on the border of Pakistan and Afghanistan is something where we need to develop a new strategy," Brown said before talking to Bush.

Brown said he would discuss the border issue with Pakistan's new president, Asif Ali Zardari, who visits Britain next week.

Bush's unusual move in personally calling the prime minister for an Afghan strategy discussion has led to speculation that the US president was trying to line up British support for the new policy, including the possible involvement of British special forces in future cross-border incursions.

Bush's executive order is certain to cause strains with some Nato allies fearful that a spreading conflict could bring down Pakistan's weak civilian government and spark a wider war. Last night there were indications of open disagreement.

James Appathurai, a Nato spokesman, said the alliance did not support cross-border attacks or deeper incursions in to Pakistani territory.

"The Nato policy, that is our mandate, ends at the border. There are no ground or air incursions by Nato forces into Pakistani territory," he said.

Nato has 53,000 troops in Afghanistan, some of which are American. But the US maintains a separate combat force dedicated to battling al-Qaida and counter-terrorism in general. Nato defence ministers are due to discuss Afghanistan in London next week.

Last week's raid, and a subsequent attack on Monday by a Predator drone firing Hellfire missiles, provoked protests across the board in Pakistan, with only Zardari among leading politicians refusing to publicly condemn it.

Pakistan's armed forces chief, General Ashfaq Parvez Kayani, said the army would defend the country's sovereignty "at all costs". He went on: "No external force is allowed to conduct operations inside Pakistan."

He denied there was any agreement or understanding to the contrary. His comments were widely interpreted as a warning to Zardari not to submit to the American importunity. But his tough words also raised the prospect of clashes between US and Pakistani forces if American military incursions continue or escalate.

Until now, Washington has regarded Pakistan as a staunch ally in the "war on terror" that was launched in 2001. But the alliance has been weakened by last month's forced resignation of the army strongman, former general Pervez Musharraf, and his replacement by Zardari, Benazir Bhutto's widower.

Polls suggest most Pakistanis favour ending all counter-terrorism cooperation with Washington, which is blamed for a rising civilian casualty toll in Afghanistan and in the tribal areas.

Yousaf Raza Gilani, Pakistan's prime minister, joined the chorus of condemnation yesterday. He reportedly told state media Kayani's warning that unilateral US actions were undermining the fight against Islamist extremism represented the government's position.

Admiral Mike Mullen, chairman of the joint chiefs, and Robert Gates, defence secretary, told Congress this week that victory in Afghanistan was by no means certain and the US needed to take the fight to the enemy inside Pakistan.

Mullen called for a "more comprehensive strategy" embracing both sides of the border. "Until we work more closely with the Pakistani government to eliminate the safe havens from which they operate, the enemy will only keep coming," he said.

US and Pakistani forces have clashed by accident in the past during operations to root out militants, although sections of the Pakistani military and intelligence services are said to harbour deep resentment about perceived American interference.