* Pakistan more cooperative but ties to militants persist
* Many gaps in knowledge about ISI activities - Mullen
* White House stands behind Pakistan despite allegations
By Adam Entous and Phil Stewart
WASHINGTON, July 26 The U.S. military and intelligence agencies believe some elements within Pakistan's intelligence service maintain contact with and may even in some cases support the Taliban and its allies, but assistance for insurgents has been slowly curtailed.
U.S. concerns about Pakistan's alleged double-dealing are nothing new, and officials who have been working with Islamabad for years to try to sideline Taliban backers within the security services said on Monday they were not shocked by the contents of leaked secret U.S. military reports.
Among the reports, which cover a more than five-year period from 2004 to the end of 2009, were unverified allegations that Pakistan allowed representatives of its Inter-Services Intelligence (ISI) agency to meet directly with the Taliban to organize militant groups that fight against U.S. soldiers.
The military reports, which the organization WikiLeaks provided to The New York Times, Britain's The Guardian newspaper and German weekly Der Spiegel and were published last weekend, also detail efforts by ISI officers to run networks of suicide bombers in Afghanistan. They allege that the ISI may have been part of a Taliban plot to assassinate Afghan President Hamid Karzai.
The revelations have raised new questions about President Barack Obama's strategy, which hinges in large part on Pakistan's cooperation to turn around the troubled nine-year-old war in Afghanistan.
A U.S. official, speaking on condition of anonymity, said Pakistan was moving in a positive direction but still sometimes used militant groups to try to increase its influence in Afghanistan and undercut arch-rival India's interests.
"The Pakistanis have made possible many of our greatest victories against al-Qaeda and its violent allies, either through active cooperation or by permitting us to take action," the official said, referring to operations that have resulted in capturing or killing of senior al Qaeda figures.
"But we're also under no illusions when it comes to the Pakistanis," the official added. "While they're absolutely critical partners, there are times and cases when their interpretation of their own national interests doesn't square entirely with ours."
WORK WITH PAKISTAN
"It's not as if they're helping us on one hand and killing us on the other. But they're not beyond trying to use select extremist groups either to build up their own influence in Afghanistan or to counter Indian influence there," he added.
A U.S. military official said Pentagon concerns about Islamabad have been well known for years.
"Are we surprised to hear these things happened? No," said the official. "But it is much different today -- not perfect -- but much better than it was."
The White House defended its close ties to Islamabad, brushing aside the allegations as old news but said the status quo was not acceptable.
"I am not going to stand here on July the 26th and tell you that all is well," White House spokesman Robert Gibbs said.
"They've taken steps. We want to continue to work with them to take more steps," he said of the need to help Pakistan eliminate militant safe havens on its territory.
The chairman of the Armed Services Committee in the House of Representatives, Democrat Ike Skelton, cautioned against using what he called "outdated reports" to paint a picture of Pakistan's alleged double dealing.
"While we still have concerns about Pakistan's efforts against the Afghan Taliban, there is no doubt that there have been significant improvements in its overall effort," he said.
Top military officials acknowledge gaps in their knowledge about ISI activities.
"There's a lot I know about the ISI and there's a lot I don't know about the ISI," Admiral Mike Mullen, chairman of the military's Joint Chiefs of Staff, said in India last week.
He said Washington voices concern about some of the ISI's links in "every single engagement" with Pakistani leaders.
Last month, General David Petraeus said some of Pakistan's ties in Afghanistan date back decades -- to when the ISI was the main conduit for Western and Arab arms and funds to the mujahideen guerrillas that battled Soviet forces in the 1980s.
"Some of those ties continue in various forms, some of them, by the way, gathering intelligence," Petraeus, who recently took over command of U.S. and NATO forces in Afghanistan, told U.S. lawmakers in June. "You have to have contact with bad guys to get intelligence on bad guys."
Washington has praised efforts by the ISI's director general to clear out Taliban supporters within the organization's ranks. But they say progress has been slower than Washington would like.
"It's an extraordinarily complex country ... It's going to take some time," Mullen said.
(Editing by Patricia Wilson and Eric Beech)