The rise of Mullah Fazlullah as the Pakistani Taliban’s leader marks not only a power shift within the militant network but also threatens to ignite fresh conflict between Islamabad and Kabul.

Mullah Fazlullah is seen in Pakistan in an undated image provided the SITE Intel Group, a U.S. analysis company. 

Associated Press

ISLAMABAD—The rise of Mullah Fazlullah as the Pakistani Taliban’s new leader marks not only a power shift within the militant network but also threatens to ignite fresh conflict between Islamabad and Kabul.

Earlier this month, a U.S. drone strike killed the Pakistani Taliban’s chief, Hakimullah Mehsud, prompting a power struggle within the movement’s ranks. For the first time in its six-year history, the group tapped a commander from outside its cradle in the North Waziristan tribal area, selecting a native of Pakistan’s settled regions near Islamabad.

Ousted by a Pakistani army operation from their home valley of Swat in 2009, Mr. Fazlullah and his men are based in Afghanistan’s mountainous Kunar and Nuristan provinces, Pakistani officials and Western diplomats say. These Afghan connections could have serious consequences for relations between Islamabad and Kabul if Pakistani Taliban militants fulfill their promise to avenge the U.S. drone strike with massive attacks on the Pakistani government and army.

Islamabad’s likely response to such bloodshed would be to launch cross-border shelling into Kunar and Nuristan, analysts and diplomats say, as well as deploy some Afghan proxies against Mr. Fazlullah.

An even greater escalation is possible now that U.S.-led forces have by and large withdrawn from that part of Afghanistan. That’s especially so because Pakistani officials and some Western diplomats believe that Mr. Fazlullah enjoys tacit support from elements of the Afghan government that seek to punish Islamabad for its traditional backing of the Afghan Taliban.

“Fazlullah is seen as being hand-in-glove with the Afghan intelligence agencies, and it won’t be long before our hands are forced,” says Saifullah Khan Mahsud, executive director of the FATA Research Center in Islamabad, a think-tank focused on Pakistan’s northwest Federally Administered Tribal Area. “I don’t rule out our incursion into Afghanistan to get him as well. The U.S. has been employing the doctrine of hot pursuit—why not us?”

Any such border violence would put the U.S., which is negotiating a bilateral security pact with Afghanistan and relies on Pakistani routes, in a particularly tough spot.

Afghanistan and the U.S. have long complained that the Afghan Taliban—a separate militant organization—run their operations from shelters in Pakistan, with apparent complicity of the Pakistani security establishment. Adding evidence to these concerns was the assassination this week of a senior financier of the Afghan Taliban-linked Haqqani network in Pakistan’s orderly capital of Islamabad.

“If there are terrorist activities in Pakistan, then there will be a blame game: The Afghans are protecting him, like we are giving shelter to the Haqqanis,” said retired Pakistani Brig. Asad Munir, who served as a senior intelligence official in the country’s troubled northwest and then as the principal secretary for security in the tribal areas along the Afghan border.

The Afghan foreign ministry spokesman Janan Mosazai said that the Afghan government won’t let terrorist groups operate from Afghan territory or use them as a tool against another country. A senior Afghan intelligence official added “there is no evidence” that Kabul is aiding Mr. Fazlullah.

Kunar province Gov. Shuja-ul-Mulk Jalala Khan also described as “just rumors” Pakistani complaints that Mr. Fazlullah is based in his province, even as he said “there is no doubt that Pakistani Taliban are present in the border districts,” operating separately from the Afghan Taliban.

Not so long ago, Western officials dismissed Pakistani claims of Kabul’s support for Pakistani Taliban as little more than a conspiracy theory. That changed last month after a U.S. raid captured the deputy leader of the Pakistani Taliban, Latif Mehsud, on a highway south of Kabul—traveling in an Afghan government convoy. Afghan officials acknowledged they had reached out to Mr. Mehsud as a possible intermediary in their efforts to seek peace talks with the Afghan Taliban, an explanation that some Western diplomats have found disingenuous.

“There is a bit of tit-for-tat going on,” one diplomat said.

A midlevel Pakistani Taliban militant said that such murky connections with Afghan intelligence were dictated by necessity. “If you fight on both sides [of the border], you need allies on at least one side,” he said. “Afghanistan believes that all the problems inside Afghanistan are because of Pakistan, and it is looking for opportunity.”

Although the Pakistani militant group acknowledges the overall authority of Afghan Taliban founder Mullah Mohammed Omar, it pursues a fundamentally different strategy, attacking the Pakistani military and seeking to dismantle the Pakistani state. The Afghan Taliban, by contrast, aren’t hostile to the Pakistani establishment, and focus their campaign on Afghan government and coalition targets.

Mr. Fazlullah is the first leader of the group, formally called Tehreek-e-Taliban Pakistan, who hails from the settled parts of Pakistan proper as opposed to the tribal areas on the Afghan border. Both of his predecessors were from the Mehsud tribe in FATA’s North Waziristan, and up until now the TTP leadership was dominated by the Mehsuds.

Back in the Swat valley, Mr. Fazlullah was dubbed “Mullah Radio” for the fiery broadcasts on a pirate radio station he had established there. His new deputy also comes from a settled area, in Swabi, even closer to the Pakistani capital.

“It is a danger for Pakistan,” says Hafiz Tahir Ashrafi, who heads the Pakistan Ulema Council, a body uniting the country’s Islamic scholars. “Before, the TTP was only in North Waziristan and among the Mehsuds. Fazlullah wants to spread it all over, and make it larger.”

A former river-crossing operator, Mr. Fazlullah, aged around 40, established a draconian regime in the Swat valley, hanging accused sinners and spies on its main market square, and forbidding television, polio vaccination, and girls’ education.

While the Pakistani army views the 2009 clearing of Swat as a success, it is apprehensive that under Mr. Fazlullah the TTP would try to destabilize the valley, known for its scenery and ski resort. Mr. Fazlullah has already taken responsibility for the September killing of a Pakistani army major-general in charge of Swat. In October 2012, his men shot Malala Yousafzai, a teenage campaigner for girls’ education.

“People of Swat are very scared. They fear that Fazlullah is very familiar with this region, and will focus on the settled areas rather than FATA,” said Zubair Torwali, a local civil-society activist and columnist. “This may embolden the Swat Taliban to regroup and begin their activities here again.”

–Habib Khan Totakhil in Kabul and Saeed Shah in Islamabad contributed to this article.