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Islamabad summoned an American diplomat on Saturday to protest over the latest US drone strike which killed seven people in northwest Pakistan, the foreign ministry said.
The missile attack in the restive North Waziristan tribal district on Friday was the first since Nawaz Sharif was sworn in as prime minister this week calling for an end to such strikes.
"It was conveyed to the US CdA (Charge d'Affaires) that the government of Pakistan strongly condemns the drone strikes which are a violation of Pakistan's sovereignty and territorial integrity," the foreign ministry statement said, calling for an immediate end to the attacks.
Richard Hoagland, the US charge d'affaires -- a senior American diplomat stationed in Pakistan -- was summoned to the foreign office on the instructions of Sharif, it said.
"It was also pointed out that the government of Pakistan has consistently maintained that drone strikes are counter-productive, entail loss of innocent civilian lives and have human rights and humanitarian implications," the statement said.
Attacks by unmanned American aircraft are deeply unpopular in Pakistan, but Washington views them as a vital tool in the fight against Taliban and Al-Qaeda militants in the lawless tribal areas along the border with Afghanistan.
Sharif's government had also publicly criticised the drone strike that killed Taliban deputy Waliur Rehman last week.
Rehman, the number two in the Tehreek-e-Taliban Pakistan (TTP) faction, died along with at least five others when a drone fired two missiles on a house in North Waziristan on May 29.
The senior leader, who had a $5 million US government bounty on his head, was killed after US President Barack Obama outlined new and more restrictive guidelines on drone use.
Washington had accused Rehman of organising attacks against US and NATO forces in Afghanistan including a suicide attack in 2009 that killed seven CIA agents.
Ties with Washington will be a key part of Sharif's tenure, particularly as NATO withdraws the bulk of its forces from Afghanistan by the end of next year after more than 12 years of war.
"It was also stressed that these drone strikes have a negative impact on the mutual desire of both countries to forge a cordial and cooperative relationship and to ensure peace and stability in the region," the foreign ministry said.
Despite Pakistan's protest over drone strikes, the commander of NATO-led forces in Afghanistan met Pakistan and Afghanistan army chiefs on Saturday in the garrison city of Rawalpindi, near Islamabad.
The Pakistani military said in a statement that ISAF Commander US General Joseph F. Dunford, Pakistani army chief General Ashfaq Kayani and Afghan army chief General Sher Muhammad Karimi discussed matters of mutual interest.
Relations between Afghanistan and Pakistan, both US allies in its battle against militants, have been strained for years despite renewed US efforts to strengthen ties.
Both countries blame each other for violence by Taliban Islamic militants plaguing both sides of their border, known as the Durand Line.
Troops of both the countries have for several times exchanged fire and are in dispute over the ownership of a site on the porous border, unmarked in places.
"The three discussed matters of mutual interest with particular emphasis on coordination measures at the Pak-Afghan Border and Standing Operating Procedures put in place to improve the Border control," the statement said.