“We’re seeing that blowback,” General Cartwright, who is retired from the military, said at the Chicago Council on Global Affairs. “If you’re trying to kill your way to a solution, no matter how precise you are, you’re going to upset people even if they’re not targeted.”

General Cartwright also expressed skepticism about the draft proposal to transfer some drone operations to the military, saying that he worried about a “blurring of the line” between soldiers and spies if the Pentagon was put in charge of drone operations in sovereign countries “outside a declared area of hostility.” He said that if there are problems with the drone program, moving it “from one part of the government to another” would not necessarily solve them.

Currently, the Pentagon has responsibility for drones in Afghanistan, Somalia and in Yemen, where the C.I.A. also runs a separate program. Because the proposal being examined by the National Security Council would most likely leave drone operations in Pakistan under the C.I.A., the practical impact of such a move in the short term would appear to be quite limited. To date, the vast majority of American drone strikes and other kinds of targeted counterterrorism strikes outside conventional wars have been carried out in Pakistan, where the C.I.A. operates on its own — 365 strikes, by the count of the Bureau of Investigative Journalism in London, compared with about 45 in Yemen and a handful in Somalia.

That would mean the greatest impact of a shift of strikes to military control would be in Yemen, where both the C.I.A. and the military’s Joint Special Operations Command have carried out strikes. Hence the move may be most important symbolically rather than practically, as a statement of the United States’ long-term intentions.

While many experts argue that the military should be better than the C.I.A. at carrying out precise lethal operations, the strikes have not always played out that way. In Yemen, for example, Mr. Obama brought the C.I.A. into the drone campaign in 2011 in part because several of the military’s strikes went awry, killing women and children and a popular deputy governor.