Obama Warns of 'Difficult' Road Ahead in Pakistan, Afghanistan

President Obama warned today that there will be more violence in Pakistan and Afghanistan, but added because the security of the two nations and the United States is linked, his administration remains committed to defeating al Qaeda in the region.

"The United States has a stake in the future of these two countries," Obama said after a meeting with Presidents Hamid Karzai of Afghanistan and Asif Ali Zardari of Pakistan. "We have learned time and again that our security is shared. It is a lesson that we learned most painfully on 9/11, and it is a lesson that we will not forget."

VIDEO: Jake Tapper on Afghanistan Pakistan meetingPlay

The three leaders met this afternoon at the White House amid growing concerns about security in Pakistan in order to discuss how the three nations can work together to stabilize the region.

Obama said the United States must provide "lasting support to democratic institutions" and help support reconstruction efforts in Pakistan while the government there battles an insurgency that threatens the country's security.

"We must do more than stand against those who would destroy Pakistan. We must stand with those who want to build Pakistan," the president said. "I want the Pakistani people to understand that America is not simply against terrorism; we are on the side of their hopes and their aspirations, because we know that the future of Pakistan must be determined by the talent, innovation and intelligence of its people."

Afghanistan's ambassador to the United States, Said T. Jawad, said in an interview with ABC News that the country is seeking specifically to improve intelligence exchange, security and trade and transit in Afghanistan.

"These talks are about getting very very specific measurable objectives set forward and then working together to achieve them and also measure our accomplishment on how far we are coming... What we are seeking is a very clear objectives -- better mechanism of exchanging information, mechanism to measure deliveries of those objectives being set by Afghanistan with the assistance of the United States," Jawad said.

Early today, Afghanistan and Pakistan signed a memorandum of understanding to develop a trade agreement between the two countries by the end of the year, an event dubbed "historic" by Secretary of State Hillary Clinton.

Karzai and Zardari met with Clinton and others at the State Department this morning to discuss how to combat the growing influence of the Taliban and al Qaeda in the two countries.

Clinton stressed the need for open lines of communication and cooperation among the three countries.

"We have made this common cause because we face a common threat," Clinton said. "And we have a common task and a common challenge. We know that each of your countries is struggling with the extremists who would destabilize and undermine democracy.

"Now, we are not perfect. No human being is. We will make mistakes. But we need to have the kind of open dialogue where we express our concerns about those mistakes," she added.

Clinton expressed her "regret" about the U.S. bombing in Afghanistan that killed dozens of civilians Tuesday and said there will be a joint investigation.

Obama said today that he made clear to Karzai that the U.S. will work with the Afghan government and international partners "to avoid civilian casualties as we help the Afghan government combat our common enemy."

National Security Advisor Gen. Jim Jones said this evening that Karzai did not ask for a suspension of U.S. air strikes while the investigation occurs but was "genuine" in his acceptance of Obama's condolences for the loss of innocent life there.

"It was clear that President Karzai was moved by that, by the president's statement, and he thanked the president for, for starting off the meeting with that -- that expression of condolence," Jones said.

Jawad explicitly said the United States was behind civilian casualties, and that more needs to be done to prevent such attacks.

"And any time civilians are killed, it's a tragedy. Everyone loses. The poor Afghan civilian getting killed is the prime victim but also the international community that's fighting terrorism in Afghanistan has the prime objective of keeping the civilians safe and on their side," he said. "So we are asking once again to come up with better measures to prevent any kind of death to the civilians, which are our most important ally in the war against terrorism in Afghanistan and in the region."

Karzai said that Afghanistan will work on its relationship with Pakistan, calling the two countries "conjoined twins" who share suffering, and said that his country will work to create a stronger partnership to work against extremism.

His counterpart, Zardari, echoed the same tone. He assured Americans and Afghans that "we will also be far more transparent in our actions," not explaining what that transparency would entail.

"This is a cancer," he said. "It needs to be done away with. Pakistan carries a huge burden, confronting al Qaeda and Taliban together, but we are up to the challenge, because we are the democracy, and democracy is the only cure to this challenge."

White House to Push Afghanistan, Pakistan to Fight Extremists

White House officials said going into the meetings that Obama will push Karzai and Zardari to commit to work more intensely and cooperatively to fight al Qaeda and other extremists.

"The core principle of this meeting is the centrality of Pakistan and Afghanistan to our own national security," a senior administration official said. "We face a common threat."

Obama held separate meetings with both Karzai and Zardari, and then met with both leaders and their delegations together.

In the evening, Vice President Joe Biden will host a dinner with Karzai and Zardari, their respective delegations and congressional leaders.

After Pakistan attempted to enter into a deal with Taliban leaders in April, ceding them the Swat Valley, the Obama administration expressed growing concerns about the stability of Pakistan, a nation with nuclear weapons.

Obama was asked at his news conference last week if he could reassure the American people that Pakistan's nuclear arsenal is secure, even with ongoing fighting with the Taliban there.

"I'm confident that we can make sure that Pakistan's nuclear arsenal is secure," he said. "Primarily, initially, because the Pakistani army, I think, recognizes the hazards of those weapons falling into the wrong hands. We've got strong military-to-military consultation and cooperation."

But Obama said last week he is "gravely concerned" about the "very fragile" civilian government in Pakistan.

Adm. Michael Mullen, chairman of the Joint Chiefs of Staff, said Monday he remains "comfortable" that Pakistan's nuclear weapons are secure and does not think those weapons could get into the hands of terrorists.

"We've invested -- we, the United States -- have invested very significantly over the last three years to work with them to improve that security. And we're satisfied, very satisfied, with that progress," he said at the Pentagon.

But Mullen added that this is a "strategic concern" that the United States and Pakistan share.

Clinton said last month that Pakistan "is basically abdicating to the Taliban and to the extremists."

"Look at why this is happening," Clinton said, testifying before Congress. "If you talk to people in Pakistan, especially in the ungoverned territories, which are increasing in number, they don't believe the state has a judiciary system that works. It's corrupt. It doesn't extend its power into the countryside."

"Swat was a real wake-up call to a lot of people in Pakistan," a senior administration official said. "We understood that and we reflected that. ... We said what we said, and they did what they did."

Pakistan Plans to Fight Back Against Taliban

The Pakistani government's deal with the Taliban in the Swat Valley fell through and now the Pakistani government is fighting back.

Testifying before the House Foreign Affairs Committee Tuesday, Richard Holbrooke, the administration's special representative for Afghanistan and Pakistan, said that Zardari told him Monday night that his army would expand its efforts to fight the encroaching Taliban, including sending troops into the Taliban-controlled Swat area.

Holbrooke regarded this as a positive development but cautioned that "we'll see how this goes."

While the United States is working with the Afghans to build up and train their troops, it is an entirely different story in Pakistan.

There, administration sources say, the issue is more one of Gen. David Petraeus, head of U.S. Central Command in Iraq, teaching the Pakistani military how to deal with a counterinsurgency.

A senior military official said Pakistan's military is largely built up for a regional conflict with India. Until the past few months, its frontier corps was underequipped and undermanned.

The United States will provide Pakistan with $400 million for counterinsurgency training and support, and equipment for counterinsurgency measures, such as night-vision goggles, helicopter support and maintenance.

But the leader of Pakistan says that's not enough.

"I need drones to be part of my arsenal," Zardari told CNN's Wolf Blitzer Tuesday. "I need that facility. I need that equipment. I need that to be my police arrangement. I need to own those."

Obama Administration Will Push for Benchmarks for Pakistan

Obama ordered a full-scale review of the policy in the region before his inauguration. As part of that new policy, released at the end of March, he pledged to hold frequent trilateral talks. The next one will be after the Afghan elections in August.

When Obama outlined new diplomatic efforts in Pakistan, he urged Congress to approve legislation to significantly increase aid to Pakistan that could be used for reconstructing projects and democracy efforts.

Senate Foreign Relations Committee Chairman John Kerry, D-Mass., and ranking member Richard Lugar, D-Ind., introduced legislation Tuesday that would provide $1.5 billion in aid every year for the next five years.

Obama cautioned in March that the U.S. aid does not constitute a "blank check" for Pakistan, noting "years of mixed results" in its anti-terrorism efforts.

"Pakistan must demonstrate its commitment to rooting out al Qaeda and the violent extremists within its borders," he said. "And we will insist that action be taken -- one way or another -- when we have intelligence about high-level terrorist targets."

Holbrooke, who will take a leadership role in many of these meetings, returned recently from a donor conference where he secured $5.5 billion in pledged aid for Pakistan, including $1 billion from Japan and $330 million from Iran.

Cabinet Members Also Meet on Range of Issues

Other issues will be addressed in these two-day trilateral talks as well, including corruption, border posts, water management, food security, job creation, trade ties, building police forces, preparing relief efforts for the future refugees who may soon be displaced as the United States intensifies military operations, and addressing their problems with a "whole of government" approach so matters aren't just handled militarily.

Today's and Thursday's meetings won't just bring the three presidents together.

The intelligence chiefs from both countries will meet with CIA director Leon Panetta at Langley; the ministers of interior will meet with Attorney General Eric Holder and FBI director Robert Mueller; the finance ministers will meet with Deputy Secretary of State Jack Lew and the agriculture ministers will meet with Agriculture Secretary Tom Vilsack.

In many cases, the Afghan and Pakistani officials have not met their counterparts from across the border, so these talks will be new for them.

"Success in one country leads to success in another," a senior administration official said.

ABC News' Huma Khan, Kirit Radia and Luis Martinez contributed to this report.