Pakistan reacted angrily today after Nato said US helicopters had crossed into its territory from Afghanistan to attack militants, claiming to have killed more than 50 Taliban fighters.

The admission that two incursions had taken place over the weekend by helicopters from the Nato-led International Security Assistance Force (Isaf), and possibly a further cross-border raid today, came after recent reports of a covert CIA military force in Afghanistan that crosses into Pakistan to kill Taliban and al-Qaida fighters.

Pakistan's foreign ministry condemned the incursions as a "clear violation and breach of the UN mandate under which Isaf operates", saying it had made a formal protest to Nato. "In the absence of immediate corrective measures, Pakistan will be constrained to consider response options," said Abdul Basit, the foreign ministry spokesman.

Although remote-controlled US "drone" planes regularly cross into Pakistan to target suspected extremists in the country's lawless tribal area, the use of manned aircraft is highly controversial in a country in which anti-Americanism runs high and widely believed conspiracy theories maintain that nuclear-armed Pakistan is the next American military target.

"This should be considered a watershed event," said Mehmood Shah, an analyst who was the top security official for the tribal area. "They [Nato] must be warned: the next time you do this, it can lead to war. Our units should be deployed to fire upon them. This border has sanctity. Nato must realise they have a mandate to operate in Afghanistan, not in Pakistan."

Nato was seeking to justify the breach of Pakistani territory as self-defence or "hot-pursuit", which have some defence under international law. Pakistan is forced into the position of having to react angrily, because if it did not, it may have profound consequences for the Pakistan eastern border with arch-enemy India. There, India could use the same logic for pursuing extremists into Pakistani territory.

The incursions will add to pressure on the fragile pro-western government in Pakistan, the survival of which is in doubt after the fallout from the country's devastating floods and a constitutional battle in the courts. Marvi Memon, an opposition member of parliament, said she would raise the issue in parliament and demanded to know if there was a deal allowing incursions.

"Self-defence is no excuse for violating Pakistani airspace and thus our sovereignty," said she said.

According to Nato, a remote Afghan military outpost in the eastern province of Khost, close to Pakistan border, came under fire on Saturday. Two US Apache helicopters responded. Reports said the aircraft then entered the Kurram part of Pakistan's tribal area.

"Two helicopters were engaged and acted in self-defence. They crossed very briefly into Pakistani territory and neutralised the threat," said Captain Ryan Donald, a spokesman for Nato. "Later in the day, two helicopters received small-arms fire and, in self-defence, returned fire. In doing so, they entered Pakistan very briefly."

Donald said 49 militants had been killed in the first incursion and four to six were killed in the second attack, according to a review of the video surveillance tapes from the helicopters. He said Nato was investigating reports of a third incursion, which took place today.

Training ground



The Afghan government has bitterly complained about Taliban insurgents using Pakistan's tribal area as a haven and a training ground. Pakistan has launched military operations against extremists in the tribal area but they have targeted Pakistan-focused fighters, not those targeting Afghanistan.

The Afghan government was circumspect about the strikes. "We do not have any formal information," spokesman Waheed Omer told the Guardian today. "Our position is that countries, training grounds, sanctuaries and financing of terrorists have to be addressed for a solution in the region. We do not believe there should be military action against any other country."

Afghanistan maintains a politically sensitive relationship with Pakistan. The Afghan president, Hamid Karzai, has been treading a fine line, seeking international action against the Pakistani-bred terror groups while trying to shore up the political relationship with the Pakistan government.

Opposition leader Dr Abdullah Abdullah told the Guardian: "Since the main bases of the Taliban and al-Qaida are there, there can be counter attacks as long as civilians are protected and not harmed. The focus should be the prevention of civilian casualties. When there is direct fire from there [across the border], one cannot hide under the rocks. When groups plan and operate with impunity, the problem cannot be contained on the Afghan side."

Separately, US drone aircraft continued their assault on suspected extremists in Pakistan. A drone flying over the North Waziristan region today reportedly fired missiles at a house in a village near the town of Mir Ali, killing at least two. The missile strike was the 20th such attack this month – the most intense barrage ever unleashed by American planes on Pakistani territory. Pakistan also officially objects to the deployment of the drones on its territory, while apparently acquiescing to it behind the scenes.