Incensed by U.S. President Barack Obama's soaring use of drones to wage a covert "assassination" campaign and the infiltration of hundreds of CIA agents, Pakistan's shaky government has demanded a halt to the attacks and more control over counterterrorism operations.
Those demands follow a bluntly critical U.S. assessment that Pakistan isn't serious about waging war on the Taliban.
It may be the most serious rift since the days immediately after Sept 11, 2001, when president George W. Bush gave Pakistan a stark choice: abandon Afghanistan's Taliban regime and be treated as a key U.S. ally or face the risk of war.
The White House insisted, however, that relations with Pakistan are sound even as it declined to deny reports of a rift.
"Co-operation between our two countries and governments has been important and continues to this day," said Mr. Obama's spokesman, Jay Carney. "You know obviously that I can't discuss specifics about intelligence operations, but I can tell you that the co-operation between our two countries is important and continues."
Pakistan's President and senior military are under pressure to be seen to be standing up to Mr. Obama after the humiliation last month of being forced to set free a CIA contractor who had gunned down two Pakistanis.
The long-smouldering antipathy of Pakistanis toward what is widely seen as U.S. arrogance, interference and efforts to strip Pakistan of its cherished nuclear arsenal exploded earlier this year when Raymond Davis, the CIA operative, shot and killed two Pakistanis in broad daylight in Lahore. That Washington extricated the shooter - claiming he enjoyed full diplomatic immunity - enraged millions of Pakistanis who demanded their government put him on trial. Instead, the victims' families were quietly paid $2.3-million.
Washington halted drone attacks during the 47 days Mr. Davis was in prison, but the day after his release a drone-fired missile killed 40 people in North Waziristan. That prompted a rare and angry public denunciation from General Ashfaq Kayani, Pakistan's senior military officer, who condemned the attack for "carelessly and callously" targeting an innocent meeting of elders. Washington said those killed were insurgents.
Pakistan wants Washington to sell it Predator and Reaper drones or, failing that unlikely event, to allow joint control over drone operations.
The Obama administration has openly accused Pakistan of failing to deliver on its promise to step up counterinsurgency efforts on its side of the Afghan border. Without a concerted effort, Mr. Obama's surge may be doomed because Taliban fighters forced out of their heartlands in Kandahar and Helmand simply slip over the border to sanctuaries in Pakistan.
Islamabad, for its part, regards the partnership with the United States as the latest chapter in a history of American duplicity that will again end with U.S. forces pulling out, leaving Pakistan to cope.
Earlier this week Pakistan's embattled President Asif Ali Zardari told The Guardian newspaper that the U.S.-led war in Afghanistan was "seriously undermining efforts to restore Pakistan's democratic institutions and economic prosperity."
Both sides distrust the other. U.S. officials suspect, but never say publicly, that Pakistan's shadowy but powerful Inter-Services Intelligence maintains close links with the Taliban and other extremist Muslim groups.
Meanwhile, many Pakistanis believe Washington treats them as an unreliable and second-rate ally, useful only as part of the effort to extricate U.S. troops from Afghanistan but not a strategic partner like archrival India.
The nightmare scenario - in both countries - is that Pakistan collapses and its nuclear arsenal falls into the hands of Islamic radicals willing to risk nuclear Armageddon in a jihad or in a war with India over Kashmir.
Coupled with the steadily increasing drone attacks - which the Pakistani government unconvincingly insists it hasn't approved - there are hundreds, perhaps thousands of CIA agents, Special Forces "trainers" and contracted security personnel deployed by Washington throughout Pakistan.
It's part of Mr. Obama's Afghanistan-Pakistan strategy, which views the conflict as a single war with operations in both countries.
Mr. Obama, who has tripled the number of U.S. troops in Afghanistan and called it "the right war" - in contrast to Iraq - has made drone strikes in Pakistan a key element of his war-winning strategy against both the Taliban and al-Qaeda. The Hellfire-firing drones target the Taliban leadership in exile and hunt al-Qaeda's Osama bin Laden and other senior figures.
The drones - piloted by remote control by U.S. pilots half a world away - don't carry the political baggage of manned warplanes because, when they occasionally crash or are shot down, there is no need to mount a high-profile rescue operation or risk a pilot being held hostage.
Tensions over the arrested CIA operative and the controversial drone strikes were exacerbated when a toughly worded White House report found Pakistan's counterinsurgency efforts had mostly failed. "There remains no clear path toward defeating the insurgency in Pakistan," according to the report to Congress on the state of the war.
Last year, U.S.-Pakistani relations dipped to a low with vital supply convoys halted following the killing of Pakistani soldiers by a U.S. attack helicopter that had "strayed" across the Afghan border.
This week's threats from Pakistan threaten to undermine the war effort even more.