ISLAMABAD (Reuters) - The U.S. warning on militants based in Pakistan, blamed by Washington for this week's attack on the U.S. Embassy in Kabul, works against counter-terrorism cooperation between the two allies, the Pakistan Foreign Ministry said on Thursday.

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

"We believe these remarks are not in line with the cooperation that exists between the two countries," Pakistan Foreign Ministry spokeswoman Tehmina Janjua told reporters.

U.S. officials suspect militants from the Haqqani network were behind Tuesday's rocket attack on the U.S. Embassy compound in the Afghan capital, 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 there was no proof of such cross-border operations.

The comments are likely to fuel tensions between uneasy allies the United States and Pakistan. Relations dropped to a low point after a unilateral U.S. special forces raid killed Osama bin Laden in a Pakistani town in May.

"Pakistan and the United States have strategic cooperation. We hope to discuss these issues in a cooperative manner," Janjua told a news conference.

Pakistani officials said it was the responsibility of U.S.-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 defense policy said the South Asian country, reliant on billions of dollars in U.S. 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."


Salim Saifullah, chairman of the Senate Committee on Foreign Affairs, said comments like Panetta's didn't help, adding that Pakistan would fight militancy cautiously.

"The United States has a temporary relationship with Afghanistan. Pakistan and Afghanistan have a permanent relationship, with a long shared history and common border," he said.

"Pakistan does not support these militants, but it will go after them carefully keeping in mind the situation on the ground."

Panetta, who was CIA director until July, has long pressed Islamabad to go after the Haqqanis, seen as the most dangerous of the Taliban-allied insurgent factions fighting U.S.-led NATO and Afghan troops in Afghanistan.

Pakistan's Directorate of Inter-Services Intelligence has long been suspected of maintaining ties with the Haqqani network, cultivated during the 1980s when Jalaluddin Haqqani was a feared battlefield commander against the Soviet Union in Afghanistan.

Pakistan says it has no links to the group.

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.

The CIA has had success targeting militants in Pakistan using drones. Last month, Admiral Mike Mullen, the top U.S. military officer, cited progress curtailing Haqqani movements within Afghanistan.

Going after Haqqani could be risky for Pakistan's army, which is already stretched fighting Taliban militants determined to topple the U.S.-backed government.

(Additional reporting by Mark Hosenball in Washington and Phil Stewart in San Francisco; Writing by Michael Georgy; Editing by Nick Macfie)

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