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Gen. Dunford also rejected the suggestion that the recent friction reflects erosion in the U.S. relationship with Afghanistan.

“We do not have a broken relationship; we do not have a lack of trust,” said Gen. Dunford, adding that none of the political dust-ups have bled over into his dealings with his Afghan security force counterparts. He said that efforts to train and advise the Afghan security forces have continued and that plans for them to be in the lead for security across the country later this summer are on track.

Gen. Dunford would not detail why the scheduled transfer of the Parwan Detention Center was delayed again and called it a difference in perspective. But he made clear that the U.S. believes it must retain the power to ensure that detainees who are deemed security threats remain in custody.

Currently, there is an Afghan administrator of the prison, which is located about an hour outside the capital, but the Americans have veto power over the release of detainees. The prisoners held under American authority do not have the right to a trial because the U.S. considers them detainees held as part of an ongoing conflict.

Regarding the move to expel the special operations forces, Gen. Dunford said he spoke with Mr. Karzai about the issue on Saturday and told him the U.S. is working on a plan to transition security in the Wardak region to Afghan forces. He would not directly say whether the commandos will stay in Wardak when the deadline to leave comes on Monday. But he said Mr. Karzai knows they are working on the plan and has not yet issued a directive to the force.

• Associated Press writers Heidi Vogt and Rahim Faiez contributed to this article.