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(Recasts with Gates' comments, edits throughout, adds bylines)
By David Morgan and Kristin Roberts
WASHINGTON, Feb 6 (Reuters) - Pakistan must learn how to fight al Qaeda and the Taliban after years of preparing for a more traditional contest with India, Pentagon chief Robert Gates said on Wednesday, reiterating a U.S. offer to help.
The U.S. defense secretary said Pakistan realized only in recent months that al Qaeda posed a threat to the government of President Pervez Musharraf. He said the assassination of former prime minister and opposition leader Benazir Bhutto in December underscored that threat.
"All of a sudden what had been a nuisance is becoming a threat to the existence of the government," Gates said.
"The Pakistani army is an army that essentially has been trained and equipped to potentially fight India. They are now going to have to reorient themselves and figure out how to do counterinsurgency," he said.
The U.S. military is growing more concerned about security in nuclear-armed Pakistan and wants to play a bigger role in the state's counterterrorism fight.
Washington already gives millions of dollars annually to Pakistan for security-related assistance -- funds that have totaled $10 billion since the Sept. 11, 2001, attacks.
But in the face of growing instability, a suicide bomb campaign and the regrouping of al Qaeda in Pakistan's tribal areas, the Pentagon has offered to step up its training of Pakistani forces as part of a new $750 million program.
Michael Vickers, assistant defense secretary for special operations and low-intensity conflict, said sites are being chosen for a five-year program to train and equip the Frontier Corps, a paramilitary unit, to confront al Qaeda and the Taliban in Pakistan's northwestern tribal region.
The Pentagon also has offered to send U.S. troops into Pakistan for joint operations with the Pakistani military in the Federally Administered Tribal Areas, or FATA, where al Qaeda has regenerated over the past 18 months.
But Pakistani leaders have publicly rejected the idea of U.S. forces operating inside Pakistan, fearing it could trigger a backlash from fiercely independent Pashtun tribes living on the border with Afghanistan -- a concern Gates said he understood.
Still, Vickers said assistance could go beyond training.
"Training assistance is very important, but could extend to some other areas as well," he said.
U.S. special forces could quietly help Pakistan with intelligence and reconnaissance, he said.
"We have a lot of capabilities that we can do in a low-visibility manner," Vickers said.
A missile attack, apparently carried out by a U.S. drone, killed a senior al Qaeda figure in the region last week, according to Pakistani and U.S. officials.
Navy Adm. Michael Mullen, chairman of the Joint Chiefs of Staff, is expected to travel to Pakistan soon to discuss the security situation.
Defense officials say there are fewer than 100 U.S. troops now in Pakistan, most involved in U.S. Embassy operations. About two dozen are involved in counterterrorism and counter-narcotics training. (Editing by Will Dunham and Eric Walsh)