When President Barack Obama came to office in 2009, it did not take his new administration long to settle on a favourite 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 and 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 minimise civilian casualties), but for practical ones. Drone strikes are undeniably effective at eliminating terrorists.

However, 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 organisations 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 Centre survey found that the percentage of Pakistanis who viewed the US as a friendly country has dropped since Obama took office — from 19 per cent in 2008 to 12 per cent this year. In Yemen, where US 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 US 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 US.

But it will be difficult to disentangle the US 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 US strikes against its enemies, but opposes strikes against extremists it considers friendly.

On those battlegrounds, argues Micah Zenko of the Council on Foreign Relations, “our drones have become the counterinsurgency air force for those governments. The real reason for most of these strikes has been to protect a regime in Pakistan or Yemen.” Nobody contests the right of the US to strike at terrorists who pose an imminent danger to US citizens.

However, when the US secretly uses armed force in another country’s internal conflict, “it sets a dangerous precedent,” he said. Is the Obama administration listening? It can be hard to tell, since most of the drone programme is shrouded in secrecy. However, in recent statements, administration officials from Obama on down have emphasised the importance of limiting the drone strikes.

“Our goal has been to focus on Al Qaida and to focus narrowly on those who would pose an imminent threat to the United States,” Obama said in a television interview in September.

“It’s not some random effort, not some unnecessarily broad effort, but a very targeted effort,” Obama’s national security adviser, Thomas Donilon, said last week. So far, Zenko and other critics say, the administration’s practice does not fully match its aspirations.

However, in a little-noticed remark, Obama proposed that Congress replace its hastily drafted Authorisation for Use of Military Force, passed in the aftermath of 9/11. “One of the things we’ve got to do is put a legal architecture in place — and we need congressional help in order to do that — to make sure that not only am I reined in, but any president’s reined in,” Obama said on October 16 on, of all places, comedian Jon Stewart’s The Daily Show.

Congress has shown no great appetite to legislate the war on terror. Members may not relish the idea of explaining to constituents why politicians should place any limits on the use of armed force against terrorists. But reining-in drones — holding them to their original use against terrorists who pose an imminent threat to the US — would be a good idea.

Doyle McManus is a columnist for the Los Angeles Times.