KABUL (Reuters) - Leadership turmoil within the Taliban since the death of the militant group’s founder has fueled closer links with foreign groups like al Qaeda, the new commander of international forces in Afghanistan said, complicating counter-terrorism efforts.

U.S. commander General for Afghanistan, John Nicholson (4th L) poses for pictures at forward operating base Gamberi, Laghman province in this April 4, 2016 file photo. REUTERS/Paul Tait/Files

In an interview with Reuters, General John Nicholson pointed to what U.S. officials saw as a shift in the Taliban’s relationship with groups that Washington considers terrorist organizations.

That could influence his assessment of plans to cut U.S. troop numbers next year, because if al Qaeda, which carried out the Sept. 11, 2001 attacks on the United States, can operate in Afghanistan with increasing freedom, it may pose a greater security threat inside the country and beyond.

That was the very reason NATO forces went into Afghanistan in the first place: to prevent al Qaeda functioning freely while the Taliban, which ruled the country until its ouster at the end of 2001, looked on.

“You see a more overt cooperation between the Taliban and these designated terrorist organizations,” Nicholson said.

“Our concern is that if the Taliban were to return, that because of their close relationships with these groups, that they would offer sanctuary to these groups.”

Nicholson is about half way though a review of plans that would see U.S. troop numbers nearly halved to 5,500 by 2017 and an end to much of the training and advice the NATO-led coalition currently provides Afghan forces fighting the Taliban.

Some U.S. politicians and Afghan commanders are urging Washington to reconsider its drawdown plans, worried that the Islamist Taliban movement poses a growing threat to security.

Public appetite for an even more prolonged deployment of U.S. forces in Afghanistan is low, partly because the conflict is seen as limited to the country itself with little risk of international spillover.

Nicholson declined to comment on the review, which will be presented in Washington by June.

But he highlighted a “greater linkage” between the Taliban and U.S.-designated terrorist group al Qaeda since the death of Taliban founder Mullah Mohammad Omar and his replacement by current leader Mullah Akhtar Mansour.

Prompted by the need to win support in a leadership battle that broke out after Omar’s death was announced last year, Nicholson said Mansour had been forced closer to groups like al Qaeda and the Haqqani network, blamed for a series of high-profile suicide attacks in Kabul.

“When Mullah Omar was alive, he maintained a public distance from al Qaeda that his successor Mullah Mansour has not,” he said. “I think this is in part because Mansour lacks the legitimacy of Omar.”

U.S.-ONLY OPERATIONS “LESS FREQUENT”

Al Qaeda, which U.S. officials have estimated has between 100-300 fighters in Afghanistan, has returned as one of the main focuses of the U.S. counter-terrorism mission in Afghanistan. Some independent assessments say that estimate is too low.

The group has been less prominent in recent years as the Taliban, numbering thousands of fighters, seized territory in a series of intense battles including, briefly, the northern city of Kunduz and, more recently, swaths of Helmand in the south.

The emergence of an offshoot of Islamic State based in eastern Afghanistan, which U.S. officials believe is mainly composed of disaffected Taliban fighters and some foreign militants, has provided a further unwanted distraction.

However, the discovery last year in the south of what U.S. officials describe as a well-established training camp featuring Taliban and al Qaeda facilities together, refocused attention on the latter, as well as the broader problem of groups using Afghanistan as a base for cross-border operations.

Six organizations are now on the State Department’s list of foreign terrorist organizations active in Afghanistan, although the Taliban are not. That means U.S. forces are more limited in the authority they have to attack the group.

“The Taliban are a medium within which these transnational groups operate,” Nicholson said, pointing to other organizations such as Laskhar-e-Taiba, a Pakistan-based militant group that normally targets India.

Whatever the outcome of Nicholson’s review, the separate U.S. counter-terrorism mission in Afghanistan will continue next year, with conventional and drone aircraft, as well as special forces troops on the ground.

U.S. officials say operations in Afghanistan have picked up in intensity following the U.S. State Department’s formal designation of Islamic State in Khorasan as a foreign terrorist organization in January.

In the first three months of the year, U.S. forces conducted nearly 100 strikes against the group, which is based mainly in Nangarhar province in eastern Afghanistan, and operations have continued at roughly the same pace since, U.S. army spokesman Brigadier General Charles Cleveland said.

Unlike al Qaeda, Islamic State is fiercely opposed to the Taliban and has directed most of its attacks against them rather than Afghan forces.

The 5,500 troops earmarked to remain in Afghanistan next year will mainly focus on counter-terrorism operations, but Afghan troops, who already conduct the bulk of missions, will take an increasing share, Nicholson said.

“We possess the capabilities here if it were necessary to do a unilateral operation,” he said, but added: “that would be less frequent”.