JUDY WOODRUFF: The United States made a new move to ease tensions with Pakistan today. It came in the form of a new five-year program of military assistance.
Margaret Warner has the story.
MARGARET WARNER: Secretary of State Clinton announced the $2 billion in aid with Pakistan's foreign minister, Shah Mehmood Qureshi, at her side.
SECRETARYOF STATE HILLARY CLINTON: The United States has no stronger partner when it comes to counterterrorism efforts against the extremists who threaten us both than Pakistan.
MARGARET WARNER: The announcement came amid wide-ranging talks involving diplomatic, trade, development and military officials from both countries, including Pakistan's powerful army chief of staff, General Ashfaq Kayani.
The new five-year military aid deal, it complements last year's $7.5 billion civilian aid package, also over five years.
Foreign Minister Qureshi welcomed the help, but also acknowledged tensions in the U.S./Pakistani relationship.
PAKISTAN FOREIGN MINISTER SHAH MEHMOOD QURESHI: We knew that, as friends and allies, we would have, at times, differences of opinion, indeed, honest disagreements. But we also knew that we have the requisite political will and robust engagement to help us resolve such momentary challenges.
MARGARET WARNER: Tensions over how to fight terrorism flared publicly late last month, when NATO helicopter gunships, flying from Afghanistan, mistakenly killed three border guards inside Pakistan's northwest tribal region.
The Pakistanis retaliated by closing a crucial border crossing for 11 days, leaving NATO convoys exposed to Taliban attacks. The incident underscored Pakistan's key role in supporting operations in Afghanistan.
But Washington is frustrated by Islamabad's unwillingness to go after Taliban havens inside its own borders. Earlier this month, in a report to Congress, the White House said, "The Pakistan military has continued to avoid military engagements that would put it in direct conflict with Afghan Taliban or al-Qaida forces."
Retired U.S. Army General Jack Keane reported much the same after a fact-finding trip for General David Petraeus, the U.S. commander in Afghanistan.
Keane spoke to PBS' Charlie Rose on Tuesday.
GEN. JACK KEANE (RET.), U.S. Army: Nothing has changed. Every day, out of those sanctuaries come forces that are killing our forces and maiming our soldiers and interfering with NATO's effort at large. That is the absolute facts of it. Some of them are -- actually receive training from Pakistan forces.
MARGARET WARNER: On Wednesday, in The New York Times, former U.S. Ambassador to Afghanistan Zalmay Khalilzad said it was time to get tougher with the Pakistanis.
"The United States should demand that Pakistan shut down all sanctuaries and military support programs for insurgents," he wrote, "or else we will carry out operations against those insurgent havens, with or without Pakistani consent."
Late this afternoon, Secretary Clinton and her counterpart downplayed reports of differences over fighting terrorism.
SHAH MEHMOOD QURESHI: Yes, there were concerns on both sides. And we shared them. And why not? And why not? -- is often misunderstood with what is reported in the media.
HILLARY CLINTON: I have nothing to add to that.
MARGARET WARNER: Despite today's good humor, it will be up to Congress to decide if today's aid package is funded.