Pakistan's borders must be respected, the country's new president said Thursday, the same day he acknowledged the Pakistani military fired at NATO helicopters after they crossed into the country from Afghanistan.

Pakistani President Asif Ali Zardari addresses the 63rd session of the UN General Assembly in New York Thursday with a photo of his assassinated wife, Benazir Bhutto, on the podium. (Richard Drew/Associated Press)

NATO reported Thursday morning that Pakistani troops fired at two International Security Assistance Force helicopters that were patrolling along the eastern Afghanistan border.

The Pakistani military said the helicopters were "well within" Pakistani territory and returned fire before flying back into Afghanistan. NATO has insisted that the two American OH-58 reconnaissance helicopters, also known as Kiowas, were conducting routine operations and did not cross into Pakistani airspace.

President Asif Ali Zardari told U.S. reporters the shots were small-arm "flares" only meant as warnings to the helicopters that they had crossed the border.

It is difficult to tell where the border is in the Tanai district, where the military checkpoint is located near the Afghanistan border, said Zardari, who made the comments during a photo session with the media New York, where he was meeting with U.S. Secretary of State Condoleezza Rice.

"Sometimes the border is so mixed that they don't realize they have crossed the border," he said.

Rice agreed "the border is very, very unclear" and described the region as "one of the most inhospitable places."

Zardari warned later in the day, however, that his country cannot allow its territory "and our sovereignty to be violated by our friends."

Appearing before the UN General Assembly, Zardari told world leaders that such attacks actually strengthen the convictions of terrorists that the U.S. and others are trying to destroy, adding that Pakistan's "people wonder whether we stand alone" in the fight against extremism.

"Unilateral actions of great powers should not inflame the passions of allies," he said.

The shooting follows a number of alleged incursions into Pakistan in the border area in recent days. A suspected U.S. spy plane also allegedly crashed inside Pakistan on Tuesday night.

Shots exchanged on ground

The U.S.-led coalition reported there were no casualties or damage to the helicopters during the incident and said the helicopters did not return fire.

A joint patrol of American and Afghan border police were moving inside the Afghanistan border, with the helicopters above them, at the time the shots were fired, said U.S. Central Command spokesman Rear Adm. Greg Smith.

The joint patrol fired toward a hilltop after the helicopters were shot at, Smith said. The exchange was "to make certain that they [the Pakistanis] realized they should stop shooting."

But the Pakistanis returned fire at the border patrol in an exchange that lasted about five minutes, he said.

NATO is in contact with the Pakistani military regarding Thursday's reported shooting, a release said.

Pakistani protesters burn a U.S. flag Thursday to condemn alleged American strikes in Pakistani tribal areas along the Afghanistan border. (K.M.Chaudary/Associated Press)

Pakistan's military spokesman, Maj.-Gen. Athar Abbas, said officials are awaiting a full report on the incident, but added Pakistani units have "very clear" orders not to fire across the border.

Abbas said last week that Pakistani field commanders have previously tolerated international forces crossing into Pakistan because of the contested nature of the mountainous frontier.

But that is no longer acceptable, Abbas said.

"The orders are clear," he said. "In case it happens again in this form, that there is a very significant detection, which is very definite, no ambiguity, across the border, on ground or in the air: open fire."

In Washington, Defence Department spokesman Bryan Whitman said the coalition has requested an explanation from Pakistan, describing the incident as "troubling."

"It would be fairly hard to mistake a helicopter flying in that region as anything but ISAF or U.S.," Whitman said.

Tensions rising between U.S., Pakistan

The U.S. and Pakistan are allies, but tensions over the alleged cross-border attacks, including suspected American missile strikes in Pakistani territory, have tested relations between the two countries.

The region along the Pakistan-Afghanistan border is a known haven for al-Qaeda and Taliban militants and Pakistani extremists who attack American and NATO troops.

Washington has urged Pakistan to assert control in the region and take stiffer action against militants in the mountainous tribal belt. But there's been growing concern in the U.S. that Pakistan is unwilling or incapable of rooting out extremists in its border region.

Some Pakistani leaders and citizens have been condemning American-led operations that have crossed the border of Afghanistan into Pakistan as a violation of the country's sovereignty. U.S. commandos conducted a raid in South Waziristan on Sept. 3.

In his first meeting with Zardari, in New York on Tuesday, President George W. Bush said the United States is only trying to help Pakistan protect itself.

Zardari responded that his country is able to find its own solutions to its problems.

With files from the Associated Press