The US military said the helicopters were within Afghanistan territory providing cover for patrols in pursuit of militants when it came under fire from Pakistani troops, resulting in the exchange of gunshots by the two sides.

Pakistan's military said its troops fired warning shots at the helicopters, which it insisted were "well within Pakistani territory."

In a speech to the UN General Assembly, Zardari said Pakistan would not tolerate violations of its sovereignty, even by its allies.

"Just as we will not let Pakistani's territory to be used by terrorists for attacks against our people and our neighbors, we cannot allow our territory and our sovereignty to be violated by our friends," he said without citing the United States or the border flareup.

"Unilateral actions of great powers should not inflame the passion of allies," he further said, cautioning that any cross border raids could be counterproductive.

The sharp words he used, even after meetings with President George W. Bush and Secretary of State Condoleezza Rice this week at the sidelines of the UN meeting, underscore significant tensions between the "war on terror" allies, diplomats said.

Zardari had previously vowed zero-tolerance for military strikes into Pakistan from NATO troops fighting Taliban and Al-Qaeda militants in Afghanistan.

Rice refused to comment on the border incident, saying she did not know the full details herself, but said, "There is a very strong view that this is a problem that had to be dealt with.

"And we are going to work very closely with this democratically elected government of Pakistan," she said.

But a State Department spokesman earlier said Washington wanted an explanation from Pakistan, commenting that "the Taliban are not flying helicopters."

"We have been in touch with the Pakistanis about this and we certainly want to have an explanation," the spokesman said.

A US official told AFP recently that Washington was frustrated with "delays and sometimes non-answers" from Islamabad regarding "actionable intelligence" on militant movements in the tribal areas in Pakistan along the border with Afghanistan, where Al-Qaeda and Taliban militants were believed to be hiding.

Relating the border shooting incident, US military spokesman Rear Admiral Gregory Smith said Pakistani soldiers at a border checkpoint were observed firing on two US OH-58 Kiowa helicopters covering a patrol of Afghan and US troops about a mile and a half inside Afghanistan.

"The ground forces then fired into the hillside nearby that checkpoint, gained their attention, which worked," Smith told AFP by telephone.

"Unfortunately, though, the Pak unit decided to shoot down a hillside at our ground forces. Our ground forces returned fire."

Smith said no one on either side was hit in the exchange, which occurred in late afternoon, and the helicopters never fired any rounds.

"The whole thing lasted about five minutes," he said. "It all ended quickly."

US and Pakistani militaries are discussing the incident.

"We have to work our way through this so that we don't have any escalation of force issues in the future," Smith said.

In Kabul, NATO's International Security Assistance Force (ISAF) also insisted that the choppers had not entered Pakistani airspace.

Zardari told reporters following talks with Rice before the UN address that Pakistani troops had fired just "flares" at the US helicopters "to make sure that they know that they have crossed the border line."

NATO is conducting by far its biggest and most complex operation in Afghanistan, where there are about 70,000 international troops, most of them deployed under the miltary alliance's banner.

Rising insurgent violence in Afghanistan has tripped alarms in Washington, which has stepped up US missile strikes in Pakistan's tribal areas and infuriated Islamabad by conducting a ground cross-border raid earlier this month.