AMERICA needs a new policy for dealing with Pakistan . First, we must recognize that the two countries’ strategic interests are in conflict, not harmony, and will remain that way as long as Pakistan’s army controls Pakistan’s strategic policies. We must contain the Pakistani Army’s ambitions until real civilian rule returns and Pakistanis set a new direction for their foreign policy.

As Adm. Mike Mullen, then the chairman of the Joint Chiefs of Staff, told a Senate committee last month, Pakistan provides critical sanctuary and support to the Afghan insurgency that we are trying to suppress. Taliban leaders meet under Pakistani protection even as we try to capture or kill them.

In 2009, I led a policy review for President Obama on Pakistan and Afghanistan . At the time, Al Qaeda was operating with virtual impunity in Pakistan, and its ally Lashkar-e-Taiba had just attacked the Indian city of Mumbai and killed at least 163 people, including 6 Americans, with help from Pakistani intelligence. Under no illusions, Mr. Obama tried to improve relations with Pakistan by increasing aid and dialogue; he also expanded drone operations to fight terrorist groups that Pakistan would not fight on its own.

It was right to try engagement, but now the approach needs reshaping. We will have to persevere in Afghanistan in the face of opposition by Pakistan.

The generals who run Pakistan have not abandoned their obsession with challenging India . They tolerate terrorists at home, seek a Taliban victory in Afghanistan and are building the world’s fastest-growing nuclear arsenal. They have sidelined and intimidated civilian leaders elected in 2008. They seem to think Pakistan is invulnerable, because they control NATO ’s supply line from Karachi to Kabul and have nuclear weapons.

The generals also think time is on their side — that NATO is doomed to give up in Afghanistan, leaving them free to act as they wish there. So they have concluded that the sooner America leaves, the better it will be for Pakistan. They want Americans and Europeans to believe the war is hopeless, so they encourage the Taliban and other militant groups to speed the withdrawal with spectacular attacks, like the Sept. 13 raid on the United States Embassy in Kabul, which killed 16 Afghan police officers and civilians.

It is time to move to a policy of containment, which would mean a more hostile relationship. But it should be a focused hostility, aimed not at hurting Pakistan’s people but at holding its army and intelligence branches accountable. When we learn that an officer from Pakistan’s Inter-Services Intelligence, or ISI, is aiding terrorism, whether in Afghanistan or India, we should put him on wanted lists, sanction him at the United Nations and, if he is dangerous enough, track him down. Putting sanctions on organizations in Pakistan has not worked in the past, but sanctioning individuals has — as the nuclear proliferator Abdul Qadeer Khan could attest.

Offering Pakistan more trade while reducing aid makes sense. When we extend traditional aid, media outlets with ties to the ISI cite the aid to weave conspiracy theories that alienate Pakistanis from us. Mr. Obama should instead announce that he is cutting tariffs on Pakistani textiles to or below the level that India and China enjoy; that would strengthen entrepreneurs and women, two groups who are outside the army’s control and who are interested in peace.

Military assistance to Pakistan should be cut deeply. Regular contacts between our officers and theirs can continue, but under no delusion that we are allies.

Osama bin Laden’s death confirmed that we can’t rely on Pakistan to take out prominent terrorists on its soil. We will still need bases in Afghanistan from which to act when we see a threat in Pakistan. But drones should be used judiciously, for very important targets.

In Afghanistan, we should not have false hopes for a political solution. We can hope that top figures among the Quetta Shura — Afghan Taliban leaders who are sheltered in Quetta, Pakistan — will be delivered to the bargaining table, but that is unlikely, since the Quetta leadership assassinated Burhanuddin Rabbani, the leader of Afghanistan’s High Peace Council and a former Afghan president, last month. The ISI will veto any Taliban peace efforts it opposes, which means any it doesn’t control. Rather than hoping for ISI help, we need to continue to build an Afghan Army that can control the insurgency with long-term NATO assistance and minimal combat troops.

Strategic dialogue with India about Pakistan is essential because it would focus the Pakistani Army’s mind. India and Pakistan are trying to improve trade and transportation links severed after they became independent in 1947, and we should encourage that. We should also increase intelligence cooperation against terrorist targets in Pakistan. And we should encourage India to be more conciliatory on Kashmir, by easing border controls and releasing prisoners.

America and Pakistan have had a tempestuous relationship for decades. For far too long we have banked on the Pakistani Army to protect our interests. Now we need to contain that army’s aggressive instincts, while helping those who want a progressive Pakistan and keeping up the fight against terrorism.

Bruce O. Riedel, a former C.I.A. officer and a senior fellow at the Brookings Institution, is the author of “Deadly Embrace: Pakistan, America and the Future of the Global Jihad.”