Two weeks after the death of Osama bin Laden, the Obama administration remains uncertain and divided over the future of its relationship with Pakistan, according to senior U.S. officials.

The discovery of the al-Qaeda leader in a city near Pakistan’s capital has pushed many in the administration beyond any willingness to tolerate Pakistan’s ambiguous connections with extremist groups. After years of ineffective American warnings, many U.S. officials are concluding that a change in policy is long overdue.

Those warnings are detailed in a series of contemporaneous written accounts, obtained by The Washington Post, chronicling three years of often-contentious meetings involving top officials of both countries. Confirmed by U.S. and Pakistani participants, the exchanges portray a circular debate in which the United States repeatedly said it had irrefutable proof of ties between Pakistani military and intelligence officials and the Afghan Taliban and other insurgents, and warned that Pakistani refusal to act against them would exact a cost.

U.S. officials have said they have no evidence top Pakistani military or civilian leaders were aware of bin Laden’s location or authorized any official support, but his residence within shouting distance of Pakistani military installations has brought relations to a crisis point.

Some officials, particularly in the White House, have advocated strong reprisals, especially if Pakistan continues to refuse access to materials left behind by U.S. commandos who scooped up all the paper and computer drives they could carry during their deadly 40-minute raid on bin Laden’s compound.

“You can’t continue business as usual,” said one of several senior administration officials who discussed the sensitive issue only on the condition of anonymity. “You have to somehow convey to the Pakistanis that they’ve arrived at a big choice.”

“People who were prepared to listen to [Pakistan’s] story for a long time are no longer prepared to listen,” the official said.

But few officials are eager to contemplate the alternatives if Pakistan makes the wrong choice. No one inside the administration, the official said, “wants to make a fast, wrong decision.”

Every available option — from limiting U.S. aid and official contacts, to unleashing more unilateral ground attacks against terrorist targets — jeopardizes existing Pakistani help, however undependable, in keeping U.S. enemies at bay. Military success and an eventual negotiated settlement of the Afghanistan war are seen as virtually impossible without some level of Pakistani buy-in.

“The fact of the matter is that we’ve been able to kill more terrorists on Pakistani soil than just about anyplace else,” President Obama said last week on CBS’s “60 Minutes.” “We could not have done that without Pakistani cooperation.”

For now, the administration is in limbo, awaiting Pakistan’s response to immediate questions about bin Laden and hoping it will engage in a more solid counterterrorism partnership in the future.

That outcome seems increasingly in doubt. In Pakistan, officials’ pledges following the bin Laden raid that Pakistan would never let its territory be used for terrorist strikes against another country have turned to heated accusations of betrayal by the United States.

There have been few high-level contacts with the Pakistanis since the raid. Telephone calls last weekend to Pakistan’s military chief Gen. Ashfaq Kayani by White House national security adviser Thomas E. Donilon and Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, were said to be inconclusive at best.

Top administration national security officials have held several meetings on Pakistan in the White House Situation Room, and more are scheduled this week. No decision has been made on whether Secretary of State Hillary Rodham Clinton will make a previously scheduled trip to Pakistan later this month.

“This is supposed to be a continuation of the strategic dialogue” Clinton started with Pakistan last year, said a senior Pakistani official who expressed rising disappointment that the civilian government has echoed the bellicose military response.

Sen. John F. Kerry (D-Mass.), who has served as go-between for the administration during previous clashes with Islamabad, traveled to the region late last week with a message of urgency from the White House and warnings about the unsettled “mood of Congress,” one U.S. official said.

While U.S. lawmakers call for reconsideration of $3.2 billion in annual U.S. aid, public outrage has grown in Pakistan as more details have emerged about the raid. Months in the planning, CIA Director Leon Panetta said it was conducted without informing Pakistan for fear of leaks or interference. Humiliated and angry, Pakistan’s powerful army and intelligence service have warned that they will “resist” any future such operations and reexamine the broad range of bilateral cooperation.

In an emotional, closed-door session of Parliament on Friday, intelligence chief Lt. Gen. Ahmed Shuja Pasha, head of the Inter-Services Intelligence agency (ISI), offered to resign after apologizing for what he said had been an intelligence lapse. It was unclear whether he was referring to the failure to intercept U.S. raiders or the discovery of bin Laden’s years-long presence near a military garrison in the city of Abbottabad.

According to U.S. and Pakistani officials, talk has resurfaced in Islamabad of ejecting up to 80 percent of the approximately 120 U.S. Special Forces troops engaged in training Pakistan’s Frontier Corps soldiers. The issue was first raised earlier this year after a CIA employee with a U.S. diplomatic passport shot and killed two Pakistanis in Lahore.

ISI control over visas issued to U.S. diplomats and intelligence officials, eased as a gesture of cooperation last year, has been reimposed, officials said.

The feeling among senior military officers is that “these Americans have let us down, they’re after us,” and involvement with the United States has “ruined our army and . . . our country,” one retired senior officer said. The military view, he said, is that “We were a very noble country before we got involved in this stupid, so-called Bush war” in Afghanistan.

According to the internal accounts, the Americans tried time and time again to convince the Pakistanis to change what former CIA official Bruce Riedel, who authored Obama’s first Afghanistan-Pakistan policy review in early 2009, called their “strategic calculus” that ties with the Pakistan-based Afghan Taliban were the only way they could maintain their strategic influence in neighboring Afghanistan.

But the accounts show consistent Pakistani suspicion that the Americans would ultimately betray them in Afghanistan, leaving Pakistan surrounded by an unfriendly government on their western border, allied with India, their historical adversary to the east.

A July 29, 2008, Washington meeting between Pakistani Prime Minister Yousaf Raza Gillani and his national security adviser, Mahmud Ali Durrani, and then-CIA Director Michael V. Hayden, his deputy Stephen R. Kappes and Anne W. Patterson, then the U.S. ambassador to Islamabad, illustrates the wariness on both sides.

The previous day, a U.S. drone-launched missile had killed Abu Khabab al-Masri, described as al-Qaeda’s chief bomb-maker and chemical weapons expert, in South Waziristan in Pakistan’s tribal region along the Afghanistan border.

Hayden apologized for collateral damage (news reports said three civilians were killed), and the strike had occurred during Gillani’s visit to the United States. The CIA director noted that the ISI had not contributed any targeting information.

Both sides referred to repeated Pakistani requests that the United States place Baitullah Mehsud, a leader of Pakistan’s increasingly lethal domestic insurgency, at the top of the hit list.

Kappes agreed that Mehsud was a legitimate target, but said that Sirajuddin Haqqani, a North Waziristan-based Afghan whose insurgent network regularly attacked U.S. forces in eastern Afghanistan, was a far higher U.S. priority.

Pakistan’s insistence that it had no intelligence on Haqqani’s whereabouts was disingenuous, Patterson said during the meeting. The ISI was in “constant touch” with him, and the madrassa where he conducted business was clearly visible from the Pakistani army garrison in North Waziristan. (Mehsud was killed in an August 2009 drone strike. Haqqani remains high on the U.S. target list.)

In a series of December 2008 meetings following the terrorist attack in Mumbai that left nearly 200 people dead — including six Americans — top Bush administration officials told Pakistan there was “irrefutable” intelligence proof that the Pakistani group Lashkar-i-Taiba was responsible.

A written communication delivered to Pakistan said that “it is clear to us that [Lashkar-i-Taiba] is responsible . . . we know that it continues to receive support, including operational support, from the Pakistani military intelligence service.”

As the Obama administration continued efforts to persuade Pakistan — while escalating the number of drone strikes — Pakistan’s ambassador to the United States, Husain Haqqani, as well as Durrani and other officials, were repeatedly told that the United States would reach a breaking point.

In a November 2009 letter to President Asif Ali Zardari, Obama offered a new level of partnership — later buttressed with increased military and economic assistance. But he warned that the existing state of affairs, with Pakistan seeing insurgent groups as proxies for influence in Afghanistan, could not continue.

The following May, a Pakistani immigrant, the son of an army officer, allegedly tried to explode a car bomb in New York’s Times Square. Subsequent investigations traced his training to Pakistani insurgent camps.

In October, Obama dropped in on a high-level White House meeting between his national security team and Kayani. Referring to the Times Square bombing attempt, Obama warned that if a successful attack in this country were traced to Pakistan, his hands would be tied in terms of the future U.S.-Pakistan relationship.

In an interview last week in Pakistan, Durrani said he was not surprised at the unilateral U.S. attack on bin Laden. “The Americans had made it clear long ago that if they find a high-value target of this level, wherever in the world [they would] go after it,” he said.

What surprised him, Durrani said, was that “it made me look stupid” after years of talks with U.S. officials in which “I kept on trumpeting at the top of my voice, ‘Osama bin Laden cannot be here.’ ”

Brulliard reported from Islamabad.