ISLAMABAD - Interior minister has said elements of the Afghan government are likely supporting a senior Pakistani Taliban leader who is fighting to topple the Islamabad government, accusations which could further raise tensions over cross-border raids by militants.

Pakistani officials say the Taliban commander known as Fazlullah has been orchestrating raids on Pakistani security forces from Afghanistan, where he fled several years ago after the army operation against his stronghold in the Swat Valley.

Pakistan has repeatedly called on Afghanistan to hunt down Fazlullah, whose fighters cross the border in their hundreds, set up ambushes and attack army checkpoints. “If somebody is living in somebody’s house and you ask him ‘who is giving you food, who is giving you all this shelter?’ You know he is in Afghanistan,” Interior Minister Rehman Malik told Reuters in a weekend interview.

“I think some of the elements (of the Afghan government) there are supporters. Maybe state actors, maybe non-state actors.” US and Afghan officials say there is no comparison between the relatively small and recent presence of Fazlullah’s men in eastern Afghanistan and what they describe as long-standing ties between elements of Pakistani intelligence and the Afghan Taliban.

Malik provided no evidence to support his assertion that elements within Afghanistan were supporting Fazlullah, nor did he give further details.

“These comments made by the Pakistani Interior Minister are irresponsible and a baseless allegation,” said Afghan Interior Ministry spokesman Sediq Sediqqi.

“Afghanistan has been under attacks from safe havens of insurgents inside Pakistan, and we are quite sure that Mullah Fazlullah is somewhere in Pakistan.”

Fazlullah and other militant leaders based along the frontier complicate US efforts to stabilise the region before most NATO combat troops withdraw from Afghanistan by the end of 2014. The issue has strained ties between Islamabad and Kabul.

Afghanistan has long accused Pakistan of backing militants said to be based on its soil who cross the border to attack Afghan and NATO forces, including the Haqqani network. Islamabad denies the allegations.

In his heyday, Fazlullah was known as “FM Mullah”, for his fiery radio speeches broadcast in Swat, which was a tourist resort before he and his men imposed a reign of terror there. A burly man in his thirties with a heavy black beard, Fazlullah dispatched his men to publicly flog and behead opponents, or anyone they deemed immoral. Fazlullah has re-emerged as a major security headache for the military, which is already stretched fighting other Taliban insurgent leaders.

“He is as dangerous (for Pakistan) as the Haqqanis are dangerous for Afghanistan. He is energising terrorism now. He is recruiting people, he is planning,” said Malik.

In June, about 100 militants loyal to Fazlullah sneaked across the border and ambushed Pakistani troops. The fighters later released a video of what they said were the heads of 17 ambushed soldiers.

It was a reminder that despite army offensives, militant leaders can simply melt away and reappear to take on army.

“Unfortunately he is enjoying his life in Afghanistan,” said Malik. “I appeal to Afghanistan to look into it and make sure (his) people don’t come to us.”

Greater cooperation on border security could be hard to achieve. There are no signs that either side will back down.

Asked if Pakistan would be willing to go after the Haqqanis, Malik said: “They are not our babies, they are no longer anyone’s babies. They have become independent.”