KABUL, Afghanistan — Two separate but similarly bitter disagreements over drone strikes in Pakistan and Afghanistan have complicated relations between the United States and those two countries at a delicate moment, again highlighting the political complications from America’s persistent reliance on the lethal remote-controlled weapons.

In Afghanistan, the American military commander called President Hamid Karzai late Thursday to apologize for a drone strike that resulted in civilian casualties and that gave Mr. Karzai renewed reason to refuse to sign a long-term security agreement with the United States.

In Pakistan’s tribal belt, meanwhile, what was thought to be C.I.A. drone strike on Friday killed a Pakistani militant days after a major political party, as part of its campaign to end the drone strikes, publicly named a man it said was America’s top spy in the country.

The use of these weapons, which is deeply resented, highlights the political costs to the United States of the drone campaigns, even as its range of military options in the region has started to narrow with American combat troops leaving Afghanistan.