Members of Pakistan's spy agency are pressing Taliban field commanders to fight the U.S. and its allies in Afghanistan, some U.S. officials and Afghan militants say, a development that undercuts a key element of the Pentagon's strategy for ending the war.

The explosive accusation is the strongest yet in a series of U.S. criticisms of Pakistan, and shows a deteriorating relationship with an essential ally in the Afghan campaign. The U.S. has provided billions of dollars in military and development aid to Pakistan for its support.

The U.S. and Afghanistan have sought to persuade midlevel Taliban commanders to lay down their weapons in exchange for jobs or cash. The most recent Afghan effort at starting a peace process took place this week in Kabul.

But few Taliban have given up the fight, officials say. Some Taliban commanders and U.S. officials say militant leaders are being pressured by officers from Pakistan's Inter-Services Intelligence agency not to surrender.

"The ISI wants to arrest commanders who are not obeying [ISI] orders," said a Taliban commander in Kunar province.

U.S. officials say they have heard similar reports from captured militants and those negotiating to lay down their arms.

A senior Pakistani official dismissed the allegation, insisting Islamabad is fighting militants, not aiding them.

"Whenever anything goes wrong in Afghanistan, ISI is to be blamed," said the senior Pakistani official. "Honestly, they see ISI agents behind every bush in Afghanistan."

The explosive accusations of ISI efforts to keep Taliban commanders on the battlefield are the strongest yet in a series of U.S. criticisms of Pakistan, and show a deteriorating relationship with an essential ally. The U.S. has provided billions of dollars in military and development aid to Pakistan in return for its support for the Afghan war and its own fight against extremists; the reports suggest some Pakistani officials are undermining that strategy.

The Taliban commander in Kunar, like others interviewed in recent days, said he remained opposed to the presence of foreign troops in Afghanistan and had no plans to stop fighting them. But "the ISI wants us to kill everyone—policemen, soldiers, engineers, teachers, civilians—just to intimidate people," the commander said.

He said he refused, and that the ISI had tried to arrest him. "Afghans are all brothers; tomorrow we could be sitting together in one room."

The allegations of interference by the Pakistani spy agency come amid a new U.S. strategic focus on Pakistan as key territory in the Afghan war.

Gen. David Petraeus, who took over in July as the top coalition commander in Afghanistan, has come to see militant havens in Pakistan, from which the Afghan Taliban and Haqqani network of radicals stage attacks in Afghanistan, as a greater threat than he had previously assessed them to be, according to officials.

In September, Gen. Petraeus said Afghan President Hamid Karzai had frequently raised the issue with him. "The biggest single issue he typically raises has to do with the sanctuaries the Taliban and Haqqani have in Pakistan. That is a concern we share. It is a concern he and I have discussed with Pakistani partners," Gen. Petraeus said.

The new assessment has supported a ramped-up campaign of Central Intelligence Agency drone strikes on militant targets across the border, including targets believed to be involved in a plot to launch attacks in Europe.

That shift has also brought debate in the U.S. about how to approach Pakistani allies. For more than a year, U.S. military officials have praised Pakistan's actions to confront militants in the tribal areas bordering Afghanistan.

But U.S. officials have been voicing frustration with what they see as Pakistan's focus on fighting extremists who pose a domestic threat while avoiding militant groups that use Pakistani havens to stage attacks across the border.

A White House report released to Congress this week painted a grim picture of the Pakistani military's ability to defeat insurgents in its tribal areas. Some Obama administration officials say the U.S. must be more forceful with Pakistan to make it clear that Washington wants more direct action against militants. Other say the public and private criticism of Islamabad is likely to backfire.

Pakistan says its forces are stretched too thin to fight all militants—particularly with some soldiers redeployed to aid relief efforts from massive flooding this summer.

The ISI helped bring the Taliban to power in Afghanistan in the 1990s. After the September 2001 terrorist attacks, Islamabad officially broke with the movement and sided with the U.S.

U.S. officials have said since then that some ISI elements maintained links to the Taliban and other Islamist extremist groups to guarantee Pakistan's influence in Afghanistan after an eventual American withdrawal.

Adm. Michael Mullen, chairman of the Joint Chiefs of Staff, has repeatedly said elements within the ISI have had ties with extremist organizations and has called on the intelligence agency to "strategically shift its focus."

But the U.S. has generally muted its concerns about ISI cooperation, in part because senior U.S. officials remain divided on whether it is coming from rogue elements within the intelligence agency or is fully sanctioned.

Some U.S. officials say the top levels of the ISI are committed to trying to reform the agency. "It is difficult to know how much the lower levels of ISI answer to senior leadership," said a military official.

Other officials are more skeptical, saying such work couldn't go on without sanction from the ISI's top officers. "I haven't seen evidence that the ISI is not in control of all of its parts," said a senior U.S. defense official.

U.S. officials say Pakistani pressure on midlevel Taliban leaders is part of Islamabad's effort to make sure it has significant leverage in peace efforts.

Those efforts range from the U.S.-backed strategy to woo the Taliban rank-and-file to attempts by the Afghan government to open high-level talks with the insurgency's leadership.

U.S. officials consider wooing Taliban fighters to be a critical part of their strategy to pacify large swaths of Afghanistan by next summer, so they can begin handing over territory to Afghan security forces and drawing down American forces.

To drive up the number of militants willing to give up the fight, the Afghan government has promised jobs or cash payouts. U.S. special operations forces also hope to organize some former militants into local police forces. And they are trying to give the process a boost by targeting militants—in effect, scaring them into defecting.

U.S. officials also say that wooing fighters could weaken the insurgency to the point where Taliban leaders would opt to open substantive peace talks with the Afghan government on terms acceptable to the West.

Much of the Taliban's top leadership is believed to live in Pakistan, and Taliban field commanders say many of their colleagues are close to the ISI.

"The ISI is supporting those under its control with money, weapons and shelter on Pakistani soil," said a Taliban commander from the southeastern province of Paktia.

U.S. officials concede that it would be hard, if not impossible, to cut a peace deal in Afghanistan without Pakistan.

But in recent months, Pakistani officials have voiced frustration with U.S. and Afghan officials for keeping them in the dark about reconciliation efforts. Pakistani officials, fearful of an Afghan regime that enjoys warm relations with archenemy India, insist they have a role in brokering any peace settlement.

—Tom Wright contributed to this article.

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Were you paying attention?

You pay taxes to the U.S. government. The U.S. government gives your money to Pakistan. Pakistan gives it to the Taliban. The Taliban uses the money to buy weapons, ammunitions and explosives to kill American G.I.s.

We've been conducting a conventional war against the Taliban for 10 years now. It seems like the only people who are getting the dirty end of the stick are the American G.I.s and the American tax payers. Maybe the time has come for someone else to feel our pain. The Taliban deserve to be exterminated just for being the stinking cockroaches that they are, crawling out of that dunghole into other countries. The Pakistanis deserve to be exterminated for being treacherous bastards, taking our money and backstabbing us. If the U.S. government was any good, the war would have been conclusively WON 8 years ago.

I'm 65 years old. The U.S. won its last war just before I was born. Every war since then has been a tie or a "no decision". Mine was Vietnam. Another generation is being screwed up now in IraqAfghaPakiFukistan. How about we airlift all our troops out of there and just nuke the jihadis?

I haven't heard any better ideas.