Pakistan's new President, Asif Ali Zardari, is facing demands to withdraw co-operation with the US in the "war on terror" amid rising anger at the increasing number of American attacks on Pakistani soil.
There have been four so far this month, including the first acknowledged ground assault by US special forces based across the border in Afghanistan.
Despite official Pakistani condemnation of the strikes, mostly by missiles fired from Predator drones, Mr Zardari is being accused by opposition parties of having secretly agreed to them. Equally damaging, it is possible that Pakistan's military chiefs were aware of US operations but did not inform him.
The row has intensified in the past week since the disclosure that President George Bush signed an order in July authorising cross-border attacks from Afghanistan without seeking Pakistani agreement.
The US has made no secret of its concern at Afghanistan's worsening instability, emphasised yesterday by the death of a provincial governor in a suicide bombing 12 miles from Kabul. The US emphasis on the militant threat from Pakistan's lawless tribal areas, where al-Qa'ida's top leaders are believed to be hiding, is part of a reassessment of US priorities in Afghanistan and Iraq.
President Bush said last week that troop levels in Iraq would remain high, with only 8,000 coming home early next year, and he announced a "quiet surge" in Afghanistan. A Marines battalion due to go to Iraq in November will be switched to Afghanistan, and an army combat brigade will follow, adding about 4,500 US troops to the 33,000 already there.
Mr Bush's statement was followed by congressional testimony from Admiral Michael Mullen, the top US military commander. He told the House Armed Services Committee: "I'm not convinced we're winning it in Afghanistan", but added he was "convinced we can" as long as there is a new strategy to address the issue of militants in Pakistan.
"These two nations are inextricably linked in a common insurgency that crosses the border between them," he said. "We can hunt down and kill extremists as they cross over the border from Pakistan... but until we work more closely with the Pakistani government to eliminate the safe havens from which they operate, the enemy will only keep coming."
The recent wave of cross-border attacks raised the question of how much co-ordination there has been with Pakistan's civilian government. On several occasions, Pakistani helicopter gunships have swept the area shortly after US missile strikes, signalling a degree of tacit acceptance by the military.
However, on 3 September, US special forces crossed near the Afghan village of Angoor Adda and attacked a Pakistani settlement only a few hundred yards from the border. At least 15 people were killed, with local people claiming some were civilians.
The anger caused by this incident grew after The New York Times disclosed Mr Bush's secret order to permit ground operations in Pakistan. It quoted a senior US official as saying: "We have to be more assertive. Orders have been given."
Pakistan's army chief, General Ashfaq Kayani, condemned the raids and denied any "agreement or understanding" that would allow Nato forces to operate on Pakistan's territory. But he attended a conference aboard USS Abraham Lincoln in the Indian Ocean last month with Admiral Mullen and top US commanders in Afghanistan.
If the US has decided to bypass Mr Zardari's civilian government, it risks exacerbating Pakistan's "significant political uncertainty", the phrase used by Admiral Mullen in his congressional testimony.
Military analysts expect the bulk of American reinforcements to be sent to eastern Afghanistan, bordering the tribal areas. But in Helmand province, where most of Britain's 8,000 troops are stationed, 2,500 US Marines sent to help early this year will not be replaced.
Bolstered by air power, the Marines drove the Taliban out of the southern district of Garmsir. They are now handing the district back to Afghan and British troops, but it remains to be seen whether these forces have the firepower to maintain the gains.