A senior Taliban commander in Pakistan is believed to have been killed by a drone strike launched by the United States, the first such operation since President Barack Obama announced tighter regulations on their use.

Two missiles were reportedly fired from the unmanned craft, hitting a house in a village near Miran Shah in North Waziristan, in an operation that will further complicate the debate over drones and present an immediate challenge for Pakistan’s prime minister elect, Nawaz Sharif, whose party campaigned against the programme in elections earlier this month.

Pakistani intelligence officials told Reuters that up to seven people were killed, among them Wali-ur-Rehman, the man considered to be No 2 in the Pakistan Taliban’s hierachy. However, there was no immediate independent verification of the claim and the Taliban denied Rehman was dead.

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US drone strikes – which usually target al-Qa’ida and Taliban fighters involved in attacks on Western troops in Afghanistan – are deeply controversial in Pakistan. A foreign ministry spokesman condemned the operation but analysts said the fact that the Americans had targeted the Pakistan Taliban, which has largely attacked targets inside Pakistan, could suggest co-operation with the Pakistani military.

While many Pakistanis are concerned about the civilians killed, there is also anger that the drones represent an affront to Pakistan’s sovereignty.

During his election campaign, Mr Sharif, who is due to be sworn in next week, said he was opposed to their use and would withdraw from the US’s so-called War on Terror. “Drones indeed are challenging our sovereignty. Of course, we have taken this matter up very seriously,” he told reporters, shortly after his election victory.

If confirmed, the death of Rehman would be a blow to the Taliban. The US has a $5m bounty out on Rehman, who Washington has accused of involvement in the 2009 suicide attack on a US base in Afghanistan that killed seven Americans working for the CIA.

White House spokesman Jay Carney said Rehman’s death would deprive the militant group of its chief military strategist involved in “horrific attacks” against both Americans in Afghanistan and Pakistani civilians and soldiers.

The strike was the first since Mr Obama delivered a speech last week in which he said that tighter regulations would be imposed on use of drones in places such as Pakistan and Yemen. It is likely that control of their use will switch from the CIA to the Pentagon, though critics point out that most details about the operation of drones remain classified.

“As our fight enters a new phase, America’s legitimate claim of self-defence cannot be the end of the discussion,” Mr Obama had said. “To say a military tactic is legal, or even effective, is not to say it is wise or moral in every instance. For the same human progress that gives us the technology to strike half a world away also demands the discipline to constrain that power, or risk abusing it.”

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Mr Sharif’s position on drones may be more nuanced than his campaign slogans suggested. Senior members of his party have said what they really want is control over their targeting.

If it is confirmed that Rehman, the deputy to the Taliban’s commander Hakimullah Mehsud, or another senior Taliban figure was killed this morning, it will strengthen the hand of those who support use of drones.

“I think Mr Sharif will be caught in a dilemma. The target that the Americans have chosen could not have been better for Pakistan,” said retired general Talat Masood, an Islamabad-based analyst.

“At the political level it may raise some questions, but he must have known after President Obama’s speech that strikes would continue.”

Mr Masood said the decision to target a Pakistani Taliban fighter “could” indicate the co-operation of the Pakistani military, but he added: “The level of co-operation between the intelligence agencies is not always clear.”

There have been 355 drone strikes since 2004, according to the US–based New America Foundation. At least 3,336 people have been killed.

Earlier this month, a court in Peshawar declared the strikes were illegal and asked the government to move a resolution against their use in the United Nations.

The court made its announcement in relation to a legal petition filed last year by the Foundation for Fundamental Rights, a legal charity based in Islamabad. It was acting on behalf of the families of up to 50 people killed when missiles stuck a tribal gathering, or jirga, in March 2011.

Profile: Wali-ur-Rehman

Wali-ur-Rehman, had been a known Taliban leader since 2005 but was only added to Washington’s list of so-called “Specially Designated Global Terrorists” in 2010, along with the top commander, Hakimullah Mehsud.

Rehman was once a spokesman for Pakistan Taliban leader Baitullah Mehsud, from the Mehsud tribe, who was killed by a drone missile strike in 2009. After that, Rehman was in line to lead the organisation but was passed over.

The man regarded as the “No 2” in the Taliban in Pakistan was reported to have died in drone strikes on at least two occasions prior to this morning’s strike.