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It was Mr. Obama’s fourth trip as president to Afghanistan, but his first since being re-elected in 2012. Also along for the trip were National Security Adviser Susan E. Rice; senior national security director for Afghanistan Jeff Eggers; senior presidential adviser Dan Pfeiffer; and counselor to the president John Podesta, who has a son serving in Afghanistan.

White House deputy national security adviser Ben Rhodes told reporters traveling with the president that the administration saw the trip as “an opportunity for the president to thank American troops and civilians for their service.” He noted that Mr. Obama had been looking for an opportunity to get to the country for some time.

Mr. Rhodes also said the scandal over the VA did not “factor into the planning for the trip.”

The Afghan political calendar also explained the decision not to meet Mr. Karzai, according to Mr. Rhodes. Two candidates for president are campaigning in a run-off election.

At least 2,181 members of the U.S. military have died during the nearly 13-year Afghan war and thousands more have been wounded. There are still about 32,800 U.S. troops in Afghanistan, down from a high of 100,000 in mid-2010, when Mr. Obama sent in additional soldiers to quell escalating violence.

As is typical of recent presidential trips to war zones, the White House did not announce Mr. Obama’s visit in advance. Media traveling with Mr. Obama for the 13-hour flight had to agree to keep the trip secret until the president arrived at the air base.

“We just don’t want to take any risks with the president’s security,” Mr. Rhodes said.

Mr. Obama has staked much of his foreign policy philosophy on ending the two wars he inherited from his predecessor, George W. Bush.

The final American troops withdrew from Iraq in the closing days of 2011 after the U.S. and Iraq failed to reach a security agreement to keep a small American residual force in the country. In the years that have followed the American withdrawal, Iraq has been battered by resurgent waves of violence.

U.S. officials say they’re trying to avoid a similar scenario in Afghanistan. While combat forces are due to depart at the end of this year, Obama administration officials have pressed to keep some troops in Afghanistan after 2014 to continue training the Afghan security forces and undertake counterterrorism missions.

Pentagon officials have pushed for as many as 10,000 troops; others in the administration favor as few as 5,000 troops. Mr. Obama has insisted he will not keep any Americans in Afghanistan without a signed security agreement that would grant those forces immunity from Afghan law.

U.S. officials had hoped plans for a post-2014 force would be well underway by this point. But Mr. Karzai stunned U.S. officials this year by saying he would not sign the security agreement even though he helped negotiate the terms. The move signaled that Mr. Karzai does not want his legacy to include a commitment to allow the deployment of international troops in his country any longer.

Mr. Karzai’s decision compounded his already tense relationship with officials in Washington who have grown increasingly frustrated by his anti-American rhetoric and decision to release prisoners over the objections of U.S. officials. Mr. Obama and Mr. Karzai have spoken just once in the past year.

By skipping a meeting with Mr. Karzai while in Afghanistan, Mr. Obama is signaling that the White House already has discounted the Afghan president as a worthwhile partner.

Before leaving Afghanistan, Mr. Obama did speak to Mr. Karzai by phone for more than 15 minutes. A White House official said Mr. Obama praised Mr. Karzai “for the progress being made by Afghan security forces.”

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