An inquiry by the Yemeni Parliament found that the strike had killed at least 41 members of two families living near the makeshift Qaeda camp. Three more civilians were killed and nine were wounded four days later when they stepped on unexploded munitions from the strike, the inquiry found.

American officials cited strained resources for decisions about some of the Yemen strikes. With the C.I.A.’s armed drones tied up with the bombing campaign in Pakistan, the officials said, cruise missiles were all that was available at the time. Drones are favored by the White House for clandestine strikes because they can linger over targets for hours or days before unleashing Hellfire missiles, reducing the risk that women, children or other noncombatants will fall victim.

The Yemen operation has raised a broader question: who should be running the shadow war? White House officials are debating whether the C.I.A. should take over the Yemen campaign as a “covert action,” which would allow the United States to carry out operations even without the approval of Yemen’s government. By law, covert action programs require presidential authorization and formal notification to the Congressional intelligence committees. No such requirements apply to the military’s so-called Special Access Programs, like the Yemen strikes.

Obama administration officials defend their efforts in Yemen. The strikes have been “conducted very methodically,” and claims of innocent civilians being killed are “very much exaggerated,” said a senior counterterrorism official. He added that comparing the nascent Yemen campaign with American drone strikes in Pakistan was unfair, since the United States has had a decade to build an intelligence network in Pakistan that feeds the drone program.

In Yemen, officials said, there is a dearth of solid intelligence about Qaeda operations. “It will take time to develop and grow that capability,” the senior official said.

On Dec. 24, another cruise missile struck in a remote valley called Rafadh, about 400 miles southeast of the Yemeni capital and two hours from the nearest paved road. The Yemeni authorities said the strike killed dozens of Qaeda operatives, including the leader of the Qaeda branch in Yemen, Nasser al-Wuhayshi, and his Saudi deputy, Said Ali al-Shihri. But officials later acknowledged that neither man was hit, and local witnesses say the missile killed five low-level Qaeda members.

The next known American strike, on March 14, was more successful, killing a Qaeda operative named Jamil al-Anbari and possibly another militant. Al Qaeda’s Yemeni branch acknowledged Mr. Anbari’s death. On June 19, the group retaliated with a lethal attack on a government security compound in Aden that left 11 people dead and said the “brigade of the martyr Jamil al-Anbari” carried it out.