US President Barack Obama smiles as he shakes hands with troops after delivering remarks at Bagram Air Base in Kabul, May 25, 2014. [Photo/Agencies]

Obama's visit to Bagram took place late on Sunday night local time. He was joined by national security adviser Susan Rice and senior adviser John Podesta, who has a son stationed in Afghanistan.

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Frayed relations between the Obama administration and the Karzai government loomed over the visit. The Afghan president rejected an invitation extended through the US embassy to meet Obama at Bagram.

"President Karzai said he would warmly welcome him if he comes to the palace but in no way he would go (to) Bagram to meet him," Abdul Karim Khurram, Karzai's chief of staff, said.

A US official said the White House was not surprised that the proposed visit did not work on short notice.

Karzai has long expressed anger at civilian deaths in Afghanistan. He told the Washington Post in an interview in March that the war in Afghanistan was not fought with his country's interests in mind.

In a statement issued before Obama's arrival in Afghanistan, Karzai criticized the US phone surveillance program, saying it violates his country's sovereignty.