SPY EYES

WASHINGTON — President Obama, apparently resigned to President Hamid Karzai’s refusal to sign a long-term security agreement with the United States before he leaves office, told him in a phone call on Tuesday that he had instructed the Pentagon to begin planning for a complete withdrawal of American troops from Afghanistan by the end of the year.

But in a message aimed less at Mr. Karzai than at whoever will replace him, Mr. Obama said that the United States was still open to leaving a limited military force behind in Afghanistan to conduct training and counterterrorism operations.

Noting that Mr. Karzai had “demonstrated that it is unlikely that he will sign” the agreement, Mr. Obama told him, in effect, that the United States would deal with the next Afghan leader. He warned Mr. Karzai that the longer it took for Afghanistan to sign the pact, known as a bilateral security agreement, or B.S.A., the smaller the residual force was likely to be.

It was the first time the leaders had spoken since last June, and for all intents and purposes, it marked the end of a relationship that had long since broken down in acrimony.

While Mr. Obama’s message was not a surprise — administration officials had concluded weeks ago that any agreement would probably come only after elections in April — the White House’s blunt description of his call with Mr. Karzai underscored the depth of the president’s frustration and the erosion of trust in the Afghan leader.

But the call also confirmed that the White House has retreated from its earlier insistence that the Afghan government sign the agreement before the elections or face the threat of a total pullout.

“Clearly, the president is putting pressure on Karzai without closing the door on B.S.A. just as he is preparing the ground for the possibility that B.S.A. may not happen,” said Vali Nasr, the dean of the Johns Hopkins School of Advanced International Studies.

Indeed, in the call with Mr. Karzai, Mr. Obama made clear that he views a residual force as a way to prevent Afghanistan from becoming once again a haven for terrorist groups.

“Should we have a B.S.A. and a willing and committed partner in the Afghan government, a limited post-2014 mission focused on training, advising, and assisting Afghan forces and going after the remnants of core Al Qaeda could be in the interests of the United States and Afghanistan,” the White House said in a statement issued after the call.

The White House had hoped to seal the security pact before a meeting this week of NATO defense ministers in Brussels, where Defense Secretary Chuck Hagel plans to discuss the logistics of the American troop reduction in Afghanistan and the shape of a potential postwar force with other alliance partners.

Military planners have faced deep uncertainty in preparing for a mission to train, advise and assist Afghan forces after combat operations officially end this year. The governments of nations that contribute troops must approve any sustained deployments months in advance.

The major candidates for president in Afghanistan have all signaled they would sign the security agreement. But if history is any guide, the April election might necessitate a runoff, which could lead to months of political uncertainty, further delaying the security deal.

A senior administration official said Mr. Obama was sending a message to Mr. Karzai that there would be a cost to further delays, both in the rising chance that the United States might go down to zero troops and in the more limited size and scope of a residual force.

Mr. Obama’s decision to look beyond Mr. Karzai, the official said, was driven by Mr. Karzai himself, who has told the administration that he believes his successor should sign the agreement because the future government will have to live with its consequences.

Appearing before troops at Fort Eustis and Langley Air Force Base near Newport News, Va., Mr. Hagel said the military would now engage seriously in contingency planning for a complete troop withdrawal, known as the “zero option.” While he held open the option of a continued troop presence after 2014, he told reporters that as long as the agreement goes unsigned, “our options narrow and narrow.”

But he declined to give another deadline for when the United States must decide that it will go down to zero. Some Afghanistan experts have criticized Mr. Obama for imposing deadlines, given the mercurial nature of the relationship between him and Mr. Karzai.

For all the tough talk, few people in the Obama administration are willing to say publicly that they believe leaving no residual force behind is a good idea, in large part because of the fear that without any American or NATO troops, Afghanistan could revert to its status as a staging ground for terrorist plots against the West.

“The preponderance of opinion across the government is that some reasonable post-2014 presence in Afghanistan is necessary to lock in our very hard-fought gains,” Michelle Flournoy, a former top Pentagon official, said in an interview.

Faced with continued uncertainty, American and NATO commanders have drawn up plans to deploy a force this summer that is tailored to assume a training mission in 2015 but also small enough to withdraw, if no deal for an enduring presence is reached. The plan would give Mr. Obama and other political leaders maximum flexibility.

Some analysts said the administration erred by tying the decision on troops too closely to its relationship with Mr. Karzai, which became toxic this month after Afghanistan released 65 prisoners that the United States said had the blood of American soldiers on their hands.

“Making it about President Karzai is simply not the right thing to do,” said Husain Haqqani, Pakistan’s former ambassador to the United States. “President Obama needs to decide what’s in America’s interest, and whether America can continue to fight global terrorism without an effective military presence in the Central and South Asian theater of war.”

By MARK LANDLER and HELENE COOPER
NEW YORK TIMES