When President Obama came to office in 2009, it didn’t take his new administration long to settle on a favorite anti-terrorist tactic: drone strikes. In his first three years in office, the number of drone strikes against targets in Pakistan and Yemen increased dramatically, from 35 in 2008 to 121 in 2010, before dropping back to 79 so far this year, according to the Long War Journal, a website that has attempted to keep track of reported strikes.

The number of people killed by the strikes — al Qaida terrorists but also local militants and, inevitably, some civilians — escalated too; estimates vary widely, but at least 3,000 have died in both countries combined.

And that has led to second thoughts, not principally for ethical reasons (officials say they have always tried to minimize civilian casualties) but for practical ones. Drone strikes are undeniably effective at eliminating terrorists. But too many drone strikes can also provoke a political backlash, recruiting as many terrorists as they kill.

Increasingly, that critique is coming not only from human-rights organizations or cautious diplomats at the State Department but from veterans of the secret war against terrorism.

“We’ve crossed a line . . . from using drones against known terrorists to using them more broadly against whole groups of militants,” Robert L. Grenier, a former CIA station chief in Pakistan, told me last week. “It plays into the narrative that portrays the United States as an enemy of Islam.”

In fact, a Pew Research Center survey found that the percentage of Pakistanis who viewed the United States as a friendly country has dropped since Obama took office, from 19 percent in 2008 to 12 percent this year.

In Yemen, where U.S. drone strikes have killed dozens of suspected terrorists, the local affiliate of al Qaida has grown, not diminished. “We’re in danger of creating more enemies than we are removing,” Grenier said.

Grenier is not alone. Henry A. Crumpton, who spurred the development of the first armed drones as the CIA’s counterterrorism chief, has said he fears the agency has fallen into an “overreliance on technology,” opting for short-term gains from drone strikes at the expense of the long-term payoff that human intelligence efforts can bring.

Inside the administration, some officials have been arguing for stricter limits on drone operations, especially to curb what are known as “signature strikes” — strikes against guerrillas in Pakistan or Yemen who appear to be members of al Qaida affiliates but who have not been identified individually.

There are even signs that some new limits have been imposed with no public announcement. In Somalia, for example, the United States has carried out no drone strikes against the al-Shabab militia since February, reportedly because the Pentagon’s general counsel ruled that the guerrillas, while undeniably a menace to the local government, posed no direct threat to the United States.

But it will be difficult to disentangle the United States and its drones from the internal conflicts of Yemen, where the administration is backing a fragile government against a local al Qaida offshoot, or Pakistan, where the military supports U.S. strikes against its enemies but opposes strikes against extremists it considers friendly.