The United States insists it has a shared interest in ending extremist violence after Islamabad accused Washington of scuttling efforts towards peace talks by killing Pakistani Taliban leader Hakimullah Mehsud in a drone strike.

Mehsud, who was under a $5 million US government bounty, was killed when a drone targeted his car in a compound in North Waziristan tribal district on Friday.

The death of its young, energetic leader represents a major setback for the Tehreek-e-Taliban Pakistan (TTP), a coalition of factions behind some of the most high-profile attacks to hit Pakistan in recent years.

But it also threatens the government's efforts to begin talks to end the TTP's bloody six-year insurgency that has left thousands of soldiers, police and civilians dead.

Interior Minister Chaudhry Nisar condemned the US strike as a "drone attack on the peace process", saying a team of religious clerics was about to meet the TTP with a view to starting peace talks when Mehsud was killed.

"Brick by brick in the last seven weeks we tried to evolve a process by which we could bring peace to Pakistan and what have you (the US) done?" he said.

"You have scuttled it on the eve, 18 hours before a formal delegation of respected ulema (religious scholars) was to fly to Miranshah and hand over this formal invitation."

A State Department official declined to confirm that Mehsud had been killed and did not specifically address Nisar's comments, saying the issue of whether to negotiate with the TTP was an internal matter for Pakistan.

"The United States and Pakistan continue to have a vital, shared strategic interest in ending extremist violence so as to build a more prosperous, stable and peaceful region," the official said.

Pakistan's foreign ministry said it had summoned US ambassador Richard Olson to protest over the drone strike that killed Mehsud and another that hit a day earlier.

The ministry statement also stressed that despite the drone strike the government was "determined to continue with efforts to engage the TTP".

Islamabad routinely condemns drone strikes as a violation of sovereignty, and Prime Minister Nawaz Sharif urged President Barack Obama to end them during White House talks in October, but summoning the ambassador is an unusual step.

Mehsud's death is the third major blow struck against the TTP by the US this year, following the killing of number two Waliur Rehman in a drone strike in May and the capture of another senior lieutenant in Afghanistan revealed last month.

Taliban meet to choose new leader

The TTP's supreme shura, or decision-making council, met Saturday to decide who should now lead the network, which emerged following a deadly 2007 military raid on the radical Red Mosque in Islamabad.

A Taliban commander told AFP the process was being held up because the meeting location keeps moving to avoid the attentions of the US drones that fly overhead almost continuously.

Candidates under consideration to take over from Mehsud include Asmatullah Shaheen Bhittani, the head of the central shura, and Khan Said, alias Sajna, who became number two after Rehman's death in May.

Senior Taliban commander Azam Tariq dismissed media reports that Said had been elected as "speculation", telling AFP a decision would be made "in the next few days".

He accused the government of running a "dual policy", supporting the US and at the same time saying it wants talks.

"Taliban will not talk with Pakistan until drone strikes are stopped," he said.

Opposition parties accused Washington of using the drone strike to stymie the peace process before talks proper had even started.

Former cricketer Imran Khan, leader of the Pakistan Tehrek-e-Insaaf (PTI) party that rules in northwestern Khyber Pakhtunkhwa province, said the strike had "sabotaged" peace talks and showed the US did not want peace in Pakistan.

The PTI said it would call an emergency session of the provincial assembly to block NATO supply convoys transiting Khyber Pakhtunkhwa on their way to Afghanistan.

Pakistan blocked all NATO supply routes through its territory for seven months in 2012 in protest at a botched US air raid that killed 24 soldiers.

For the United States, Mehsud's death will represent a success for the CIA's drone programme at a time when it is under intense scrutiny over civilian casualties.

But the killing has prompted fears of TTP reprisals, as happened after the death of founder Baitullah Mehsud in 2009.

The TTP has risen to become arguably the biggest security threat facing Pakistan. It was behind the 2008 bombing of the Islamabad Marriott hotel and the attempt to kill schoolgirl activist Malala Yousafzai last year.

The TTP also claimed the 2010 Times Square bomb plot after training Pakistani-American Faisal Shahzad.