The build-up of 1,000 Al Qaeda fighters on the border towns of Pakistan has Pentagon officials worried, particularly since Pakistan, which has been a supportive ally in the war against terror, is preoccupied with its building brinkmanship with India over the ongoing dispute for the embattled territory of Kashmir.

News of an Al Qaeda build-up was first reported in a Monday New York Times interview with General Buster Hagenbeck, the U.S. commander in Afghanistan. At a Pentagon briefing Tuesday, Brig. Gen. John Rosa would not give specific numbers of fighters, but seemed to back up Hagenbeck's estimates.

"So what are we supposed to make of his comments? Well, he's a commander in the field. I'd believe what he has to say," said Rosa, deputy operations director for the Joint Chiefs of Staff.

The concession that growing numbers of Al Qaeda fighters may be using tribal Pakistan as a refuge from U.S. forces comes at a particularly sensitive time in Pakistani-Indian relations. Pakistan tested a nuclear missile capable of hitting Indian territory Tuesday, its third test since Saturday.

The provocation has put India on alert, leading to a further build-up of troops from both countries along their shared border.

U.S. officials fear the move may force Pakistan to drop its assistance to the United States and its war against terror.

U.S. officials "are encouraging Pakistan to remain involved ... in the war on terrorism," Pentagon spokeswoman Victoria Clarke said Tuesday.

Signs are already mounting that Pakistan's military is preparing to move troops to the Kashmir border, said a defense official.

"It is a concern when they have to focus attention and people to other parts of the country," Clarke said. "It is not helpful when their attention and some of these people have to be focused on other areas."

"It's got us concerned," Rosa said.

Assistant Secretary of State Richard Armitage is headed to the region later this week to try to bring down tensions between India and Pakistan, and Clarke said Defense Secretary Donald H. Rumsfeld had been trying to reach India's defense minister by telephone.

Indian Defense Minister George Fernandes asserted this week that some of the militants fighting for Pakistani control of Kashmir are members of Usama bin Laden's Al Qaeda terrorist network and Taliban fighters. India has also denounced the policies of Pakistani President Gen. Pervez Musharraf as "dangerous."

Musharraf, who seized control of Pakistan in a bloodless coup in October 1999 and then won a popular vote last month despite charges of holding undemocratic elections, has accused India of tyranny and repression in Kashmir, and repeated Pakistan's hope of liberating the territory.

"Pakistan will not be the one to initiate war, we want peace in the region," Musharraf said in a televised speech Monday night. "I urge the world community to ask India to move towards normalization of relations."

India has made accusations of terrorists in Kashmir before, but a Bush administration official, speaking on condition of anonymity, did not dismiss the claim, saying Al Qaeda's reach is far. The administration does not know if any of terrorists have fled to Kashmir, the official said.

Clarke and Rosa said the U.S. military has no plans to pull back the thousands of U.S. military personnel in the general region. They could potentially be affected if India and Pakistan fired nuclear weapons at each other.

Fox News' Bret Baier and William LaJeunesse and the Associated Press contributed to this report.