The Pakistani military said the troops had fired warning shots at two helicopters which were "well within Pakistani territory". NATO's International Security Assistance Force (ISAF) insisted however that the choppers had not entered Pakistani airspace. "ISAF helicopters received small-arms fire from a Pakistan military checkpoint along the border near Tanai district, Khost, September 25 while conducting routine operations in Afghanistan," ISAF said in a statement. "There are no reports of any damages to the helicopters or any casualties." The statement added: "ISAF forces and the Pakistani military are working together to resolve the matter." The district borders Pakistan's North Waziristan, one of the areas where Taliban and Al-Qaeda militants are said to have bases. The Pakistani military said the choppers had crossed into Pakistan at the Ghulam Khan area of North Waziristan. "They passed over our checkpost so our troops fired warning shots," chief Pakistani military spokesman Major General Athar Abbas told AFP. "The helicopters returned fire but there was no damage on the ground." A separate military statement said the helicopters were "well within Pakistani territory" when the incident happened. Abbas said the matter was being taken up with ISAF through the usual channels between the force and the Pakistani military. Pakistan's army is also currently investigating the crash of a suspected unmanned US spy plane 24 hours earlier near the Afghan border. Residents said it was shot down by tribesmen, but the military said it malfunctioned. Pakistani troops on Sunday also fired warning shots to repel two US helicopter gunships. With tensions high, the Pentagon quickly reacted to Thursday's shooting saying it was "an unfortunate misunderstanding." The US military "contacted the Pakistani military immediately after the incident from what I understand and they are working to ensure that the coordination measures are such that that doesn't happen in the future," Pentagon spokesman Bryan Whitman said. Most of the soldiers in eastern Afghanistan are from the US army. Tensions across the porous frontier soared after a series of US missile strikes on Al-Qaeda-linked militants and an incursion by US soldiers into Pakistani tribal areas adjoining Afghanistan. NATO has nearly 50,000 troops working in Afghanistan to help stabilise the country and defeat a growing insurgency led by the Taliban, who have links with extremists in Pakistan. However the mandate of ISAF ends at the border, although it reserves the right to self-defence. The US-led coalition also operating in Afghanistan also denies carrying out operations across the frontier. Pakistan's tribal regions have been wracked by violence since thousands of Taliban and Al-Qaeda rebels sneaked into the country after the US-led invasion of Afghanistan in late 2001. Afghanistan has long been calling for international troops to pay more attention to militants bases across the border which it says supply a steady stream of militants who are staging attacks on Afghan and international forces. But Pakistani Prime Minister Yousuf Raza Gilani Wednesday reiterated that his country would not tolerate violations of its sovereignty. "I want to declare categorically that we will not tolerate the violation of our sovereignty and territorial integrity by anyone in the name of combating terrorism," Gilani said at a dinner in Islamabad. Under growing pressure to crack down on the militants, the country has stepped up its own offensives. At least 16 Al-Qaeda-linked militants and two civilians were killed Thursday when Pakistani helicopter gunships shelled rebel hideouts in the tribal Bajaur region, which is north of Waziristan.