Just days after Barack Obama announced new restrictions on the use of drones, one of the CIA's unmanned aircraft is reported to have killed the deputy leader of the Pakistani Taliban – one of the most significant strikes for the controversial programme in months.

It was the first drone strike since Pakistanis voted overwhelmingly on 11 May for political parties strongly opposed to the US use of drones.

It could complicate the first days in office of Nawaz Sharif, the incoming prime minister who has vowed to open peace talks with insurgents and is due to assume office on 5 June.

Pakistani security officials claimed Wali ur-Rehman was among the four people killed when a missile launched in the early hours of Wednesday from a drone struck a house in Chamsa, a village a mile from Miranshah, the political capital of North Waziristan, a Taliban stronghold.

However, the Taliban refused to concede the death of Rehman, the most senior military commander of the Tehreek-e-Taliban Pakistan (TTP). A man claiming to be Rehman's driver also vociferously denied that the leader had been killed, but admitted other militants had died in the missile strike.

In recent years, militants, particularly senior leaders, have taken great pains to avoid congregating in houses, in efforts to protect themselves from strikes in North Waziristan. However, in 2013 the number of strikes has steeply declined.

Information about drone strikes is notoriously hard to verify. The Pakistani military and insurgent groups prevent journalists and investigators from visiting attack sites. Claims by intelligence sources can be inaccurate or deliberately designed to deceive.

Despite media reports suggesting Obama intended to severely rein in the use of lethal drone strikes, the president made clear in an address at the National Defence University last week that they would have to continue in Pakistan in the runup to the end of the Nato combat mission in Afghanistan next year.

He said drones were needed to kill senior al-Qaida leaders who could not be captured, but also "against forces that are massing to support attacks on coalition forces" in Afghanistan.

Pakistan's foreign ministry released a statement repeating a familiar stance on drone attacks that the government has long publicly opposed, despite considerable evidence of past complicity in the programme.

It said: "The government of Pakistan has consistently maintained that the drone strikes are counterproductive, entail loss of innocent civilian lives, have human rights and humanitarian implications and violate the principles of national sovereignty, territorial integrity and international law."

But there will be few among Pakistan's security officials who will mourn the death of Rehman, who has been responsible for huge amounts of bloodshed in Pakistan, including many deadly attacks on soldiers battling insurgency in the country.

Although Hakimullah Mehsud is head of the TTP, analysts say Rehman has been in charge of much of its activities, particularly planning and ordering attacks. He was the alleged mastermind of the bombing of the Marriott Hotel in Islamabad in 2008 that killed more than 50 people. In 2009, Pakistan offered a bounty for anyone who captured him, dead or alive.

Although primarily focused on attacking the Pakistani state, Rehman has also been involved in assaults on US forces in Afghanistan, including an attack on a US base in Khost in 2009 that killed seven Americans.

That means he fulfils one of the conditions in an unclassified summary of the new guidelines drawn up by the White House: that a target "poses a continuing, imminent threat to US persons".

The document also said drone strikes would only be used when capture "is not feasible" and "no other reasonable alternative exists to address the threat effectively".

In 2010, the US declared Rehman a "specially designated global terrorist" and offered a $5m reward for information leading to his arrest.

On the campaign trail, Sharif complained about the lethal strikes, saying they breached the sovereignty of Pakistan, although he was not as outspoken as his opponent Imran Khan, who vowed to shoot down US drones if he were elected.

Sharif has also announced his intention to engage the TTP in peace talks, and has approached an extremist mullah with strong Taliban links to act as an envoy.

On Wednesday the country's political TV talk shows gave little prominence to the first drone strike since the historic elections, focusing instead on national issues.

Some of the political heat had already been removed from the issue after the frequency of drone attacks fell dramatically this year. There have also been far fewer credible reports of civilian casualties, with many analysts suggesting the programme has become more accurate.

Pakistan has been hit by 355 such attacks since 2004, according to the New America Foundation, a US-based thinktank.

Last Thursday Obama promised strikes would fall further as Nato troops leave Afghanistan and because of the success of US policy in reducing the strength of al-Qaida.