ISLAMABAD: The US warning on militants based in Pakistan goes against counter-terrorism cooperation between the two allies, the foreign ministry said on Thursday.

“We believe these remarks are not in line with the cooperation that exists between the two countries,” said Foreign Ministry spokeswoman Tehmina Janjua.

She was referring to comments by Defence Secretary Leon Panetta that the United States would do whatever it takes to defend American forces in Afghanistan from Pakistan-based militants.

US officials, including Panetta, suspect militants from the Haqqani network were behind Tuesday's rocket attack on the US Embassy compound in Kabul, as well as a truck bomb last Saturday that wounded 77 American forces.

“Time and again we've urged the Pakistanis to exercise their influence over these kinds of attacks from the Haqqanis. And we have made very little progress in that area,” Panetta told reporters flying with him to San Francisco on Wednesday.

“I think the message they need to know is: we're going to do everything we can to defend our forces.”

Pakistani officials said it was the responsibility of US-led forces to crack down on militants when they enter Afghanistan.

“We are using all our resources to fight terrorism. As far as these issues like Haqqani network launching attacks from Pakistani territory is concerned, has any proof ever been given?” said a senior Pakistani military official who asked not to be named.

A senior Pakistani government official involved in defence policy said the South Asian country, reliant on billions of dollars in US aid, was doing all it could to stop militants from crossing the border to Afghanistan.

“But if the militants are doing something inside Afghanistan, then it is the responsibility of the Afghan and Western forces to hold them on the borders,” he said.

“They let everyone go scot-free on their side (of the border) and then they say Pakistan is not doing enough.”

Panetta said he was concerned about the Haqqanis' ability to attack American troops and then “escape back into what is a safe haven in Pakistan”.

“And that's unacceptable,” Panetta said.

Some US officials in Washington said relations were still heavily strained.

“The bilateral relationship is still in deep trouble but the atmospherics are a bit better. Name calling has largely ended for now,” said former senior CIA analyst Bruce Riedel, who has advised Obama on policy in South Asia.

“Distrust has not gone away, nor has the fundamental difference in the approach to terror.