The strained spy relationship between Pakistan and the U.S. is "of late… on the upswing," according to America's top intelligence official.

"I have to be careful what I say here," Director of National Intelligence James Clapper told students at the University of Georgia today. "First I'll say that Pakistan is a very important ally, partner - particularly as we draw down in Afghanistan and won't have the presence there that we've had in the past, whatever form that takes…"

"Many times our interests converge and sometimes they don't," Clapper said, adding that while thousands of Pakistani citizens have been killed or injured because of domestic militant actions, for the Pakistani government and its Inter-Services Intelligence agency (ISI), neighboring India is their greatest strategic concern.

"When we can converge with our interests, particularly in the intelligence realm - [I] can't say too much about that publicly - we do. Of late, particularly with the new government in Pakistan, I think that cooperation has been on the upswing," he said.

Michael Birmingham, spokesperson for the Office of the Director of National Intelligence, declined to expand on his boss's comments except to tell ABC News Clapper "was referring to the strong ongoing dialogue we have with Pakistan, including through our revitalized strategic dialogue, regarding all aspects of our bilateral relationship and shared interests, to include intelligence and security issues."

America has for years had a complex relationship with Pakistani security forces - critical to U.S. counter-terrorism efforts - which was crystallized by the extremely guarded stance the CIA took towards its counterpart, the ISI. American officials have accused the ISI of using terrorist groups in Pakistan to their own ends, even if it means targeting Americans.

In September 2011, then-Joint Chief of Staff chairman Adm. Mike Mullen testified before Congress that the Haqqani network, a Taliban-linked group designated by the U.S. as a terrorist organization, was a "veritable arm" of the ISI and that the Pakistani government was responsible for "exporting violence" to Afghanistan, including what he alleged to be an ISI-supported attack on the U.S. Embassy in Kabul. The Pakistani government denied the charges.

The relationship between the U.S. and Pakistani intelligence was already at its lowest after May 2011 when a team of U.S. Navy SEALs killed al Qaeda leader Osama bin Laden in his home in Abbottabad, Pakistan, where he had lived for at least six years less than a mile from one of Pakistan's most elite military academies. Immediately speculation ran rampant that Pakistan and the ISI must have known the terror leader was there.

"I think that at high levels - high levels being the intelligence service - at high levels they knew it," Sen. Carl Levin, Chairman of the Senate Armed Services Committee, told ABC News' Jon Karl just days after the raid. "I can't prove it. I just think it's counterintuitive not to."

Then-CIA Director Leon Panetta later told CBS News' "60 Minutes" in early 2012 that he "personally felt" that "somebody must have had some sense of what was happening at this compound."

Panetta also said the U.S. didn't warn Pakistan about the raid ahead of time because the U.S. government feared "that if we, in fact, brought [Pakistan] into it, that they might… give bin Laden a heads up." Panetta said, however, that he had no proof of Pakistani collusion with bin Laden.

The U.S. has never proved any Pakistani officials knew of bin Laden's whereabouts, and sources previously said communications intercepted by American intelligence immediately after the raid indicated bin Laden's presence had taken top Pakistani officials by surprise.

Last year the Pakistani government accused its political and military leaders of " gross incompetence" in allowing bin Laden to evade capture for so long in Pakistan, according to a leaked copy of the Abbottabad Commission report as published by Al Jazeera, but did not accuse anyone of working with bin Laden.

Still, documents concerning America's top secret intelligence budget, leaked by former NSA contractor Edward Snowden and published by The Washington Post last year, indicated a deep distrust in Pakistan and showed that the U.S. repeatedly lumped its ally in with other "key [intelligence] targets" like Iran, Russia and North Korea.

For its part, Pakistan for years has publicly condemned the CIA's use of drone strikes within its borders. Ahead of a meeting with President Obama in October, Pakistani Prime Minister Nawaz Sharif said the issue of drone strikes had "become a major irritant in our bilateral relationship…"

Later sitting with Sharif, Obama told reporters the two had "talked about security" and said they were "committed to working together and making sure that rather than this being a source of tension… that it can be a source of strength."

Birmingham declined to identify exactly to whom the intelligence director was referring today when he attributed the "upswing" in relations Pakistan's "new government." In March 2012 Pakistan appointed a new chief of intelligence, Lt. Gen. Zaheerul Islam, who between 2008 and 2010 held the position of deputy head of the ISI. In July 2013 Pakistan elected Mamnoon Hussain, a textiles magnate, as its newest president. Hussain took office in September.

Pakistani media reported in February that CIA Director John Brennan made a secret visit to Pakistan and had met with top Pakistani military officials, reportedly including Islam. Pakistan's The News noted that the meeting was the latest high-level interaction between Pakistani and U.S. officials in recent months, a development the paper said was a "positive change" signaling the "improving nature of the relationship between the two estranged allies…"

While cautious not to overstate how much the situation has changed since 2011, other U.S. intelligence officials told ABC News they shared Clapper's view of "improved relations."

ABC News' James Gordon Meek and the Associated Press contributed to this report.