SPY EYES

The Central Intelligence Agency has made a series of secret concessions in its drone campaign after military and diplomatic officials complained large strikes were damaging the fragile U.S. relationship with Pakistan.

The covert drones are credited with killing hundreds of suspected militants, and few U.S. officials have publicly criticized the campaign, or its rapid expansion under President Barack Obama. Behind the scenes, however, many key U.S. military and State Department officials demanded more-selective strikes. That pitted them against CIA brass who want a free hand to pursue suspected militants.

The disputes over drones became so protracted that the White House launched a review over the summer, in which Mr. Obama intervened.

The review ultimately affirmed support for the underlying CIA program. But a senior official said: "The bar has been raised. Inside CIA, there is a recognition you need to be damn sure it's worth it."

Among the changes: The State Department won greater sway in strike decisions; Pakistani leaders got advance notice about more operations; and the CIA agreed to suspend operations when Pakistani officials visit the U.S.

The Pakistan drone debate already seems to be influencing thinking about the U.S. use of drones elsewhere in the world. In Yemen, the CIA used the pilotless aircraft in September to kill American-born cleric Anwar al-Awlaki, a suspected terrorist. But the White House has for now barred the CIA from attacking large groups of unidentified lower-level militants there.

The CIA concessions were detailed by high-level officials in a series of interviews with The Wall Street Journal. But in a measure of the discord, administration officials have different interpretations about the outcome of the White House review. While some cast the concessions as a "new phase" in which the CIA would weigh diplomacy more heavily in its activities, others said the impact was minimal and that the bar for vetting targets has been consistently high.

"Even if there are added considerations, the program—which still has strong support in Washington—remains as aggressive as ever," said a U.S. official.

Last year, Mr. Obama expanded the CIA program to 14 drone "orbits." Each orbit usually includes three drones, sufficient to provide constant surveillance over tribal areas of Pakistan. The CIA's fleet of drones includes Predators and larger Reapers. The drones carry Hellfire missiles and sometimes bigger bombs, can soar to an altitude of 50,000 feet and reach cruise speeds of up to 230 miles per hour.

The drone program over the past decade has moved from a technological oddity to a key element of U.S. national-security policy. The campaign has killed more than 1,500 suspected militants on Pakistani soil since Mr. Obama took office in 2009, according to government officials.

To some degree, the program has become a victim of its own success. Critics question whether aggressive tactics are necessary following the eradication of senior al Qaeda leaders in Pakistan, including Osama bin Laden, killed in a helicopter raid by Navy Seals in May after drone and satellite surveillance of the compound where he was living.

Many officials at the Pentagon and State Department privately argued the CIA pays too little attention to the diplomatic costs of air strikes that kill large groups of low-level fighters. Such strikes inflame Pakistani public opinion. Observers point to the rising power in Pakistan of political figures like Imran Khan, who held large rallies to protest the drones and could challenge the current government.

All this comes at a time when the State Department is trying to enlist Pakistan's help in advancing peace talks with the Taliban, a key element of a White House drive to end the war in neighboring Afghanistan. Top officials of the CIA, Pentagon, State Department and National Security Council have been pulled into the debate. Among those voicing concerns was Gen. David Petraeus, who commanded the war in Afghanistan before becoming CIA director in September. A senior intelligence official said Gen. Petraeus voiced "caution against strikes on large groups of fighters."

Changing the handling of the drone program doesn't mean the CIA is pulling back. The agency in recent weeks has intensified strikes in Pakistan focusing on the militant Haqqani network, a group believed to be behind a series of attacks in Afghanistan. The Pentagon and State Department have backed those strikes as serving U.S. interests.

The debate in Washington was fueled by a particularly deadly drone strike on March 17. It came at a low point in U.S.-Pakistani relations, just a day after Pakistan agreed after weeks of U.S. pressure to release a CIA contractor who had killed two Pakistanis.

Infuriated Pakistani leaders put the death toll from the drone strike at more than 40, including innocent civilians. American officials say about 20 were killed, all militants.

The March 17 attack was a "signature" strike, one of two types used by the CIA, and the most controversial within the administration. Signature strikes target groups of men believed to be militants associated with terrorist groups, but whose identities aren't always known. The bulk of CIA's drone strikes are signature strikes.

The second type of drone strike, known as a "personality" strike, targets known terrorist leaders and has faced less internal scrutiny.

Signature strikes were first used under former President George W. Bush. His administration began arming unmanned aircraft to hunt al Qaeda leaders in Afghanistan immediately after the Sept. 11 attacks. As al Qaeda militants fled to Pakistan, the CIA began a secret drone program there, with quiet backing from Islamabad.

For the first years, U.S. officials used drones only to target known, top terror suspects. The drone strikes quickly became unpopular with the Pakistani public. In 2008, when Pakistani leaders bowed to public pressure and began to block U.S. requests for strikes, President Bush authorized a major expansion, allowing the CIA to conduct strikes, including signature strikes, without Pakistani permission.

Initially, the CIA was skeptical of the value of expending resources on lower-level operatives through signature strikes, a former senior intelligence official said. Military officials, however, favored the idea. The debate eventually would lead to the CIA and the military reversing their initial positions.

Mr. Obama was an early convert to drones. The CIA has had freedom to decide who to target and when to strike. The White House usually is notified immediately after signature strikes take place, not beforehand, a senior U.S. official said.

The program had some early skeptics, but their concerns gained little traction. Dennis Blair, Mr. Obama's first director of national intelligence, recommended that the CIA measure the program's effectiveness beyond numbers of dead militants, U.S. officials said. It didn't happen.

The CIA and the State Department had been at odds for months over the use of drones. Tensions flared with the arrival in Islamabad late last year of a new ambassador, Cameron Munter, who advocated more judicious use of signature strikes, senior officials said.

On at least two occasions, Leon Panetta, then the CIA director, ignored Mr. Munter's objections to planned strikes, a senior official said. One came just hours after Sen. John Kerry, the Democratic chairman of the Senate Foreign Relations Committee, visited Islamabad.

State Department diplomats weren't alone in their concerns. Adm. Mike Mullen, then the chairman of the Joint Chiefs of Staff, and other military leaders, who initially favored more aggressive CIA methods, began to question that approach.

The debate erupted after the March 17 strike, when National Security Advisor Tom Donilon and others at the White House, taken aback by the number of casualties and Pakistan's sharp reaction, questioned whether the CIA should for large groups, at times, hold its fire. Officials asked what precautions were being taken to aim at highly valued targets, rather than foot soldiers.

"Donilon and others said, 'O.K., I got it; it's war and it's confusing. Are we doing everything we can to make sure we are focused on the target sets we want?'" said a participant in the discussions. "You can kill these foot soldiers all day, every day and you wouldn't change the course of the war."

A senior Obama administration official declined to comment on Mr. Donilon's closed-door discussions but said that he wasn't second-guessing the CIA's targeting methodology and pointed to his long-standing support for the program. The official said the White House wanted to use the drone program smartly to pick off al Qaeda leaders and the Haqqanis. "It's about keeping our eyes on the ball," the official said.

In the spring, military leaders increasingly found themselves on the phone with Mr. Panetta and his deputy urging restraint in drone attacks, particularly during periods when the U.S. was engaging in high-level diplomatic exchanges with Pakistan. "Whenever they got a shot [for a drone attack], they just took it, regardless of what else was happening in the world," a senior official said.

Mr. Panetta made his first concession in an April meeting with his Pakistani counterpart. He told Lt. Gen. Ahmad Shuja Pasha that the U.S. would tell the Pakistanis ahead of time about strikes expected to kill more than 20 militants, officials said.

The debate over the future of the drone program intensified after the death of Osama bin Laden the next month. Pakistani leaders were embarrassed that the U.S. carried out the operation in their country, undetected. They demanded an end to the signature drone strikes.

Mr. Donilon, the National Security Advisor, launched a broad review of Pakistan policy, including the drone program. Officials said the internal debate that ensued was the most serious since the signature strikes were expanded in 2008.

CIA officials defended the signature strikes by saying they frequently netted top terrorists, not just foot soldiers. Twice as many wanted terrorists have been killed in signature strikes than in personality strikes, a U.S. counterterrorism official said.

Adm. Mullen argued that the CIA needed to be more selective. Then-Defense Secretary Robert Gates feared that the Pakistanis, if pushed too hard, would block the flow of supplies to troops in Afghanistan, officials said.

For Secretary of State Hillary Clinton, who has supported the CIA's strikes in the vast majority of cases, the biggest focus has been to make sure political ramifications are properly assessed to avoid a situation where the political opposition in Pakistan becomes so great that the country's current or future leaders decide to bar the drones outright.

Independent information about who the CIA kills in signature strikes in Pakistan is scarce. The agency tells U.S. and Pakistani officials that there have been very few civilian deaths—only 60 over the years. But some senior officials in both governments privately say they are skeptical that civilian deaths have been that low.

Some top officials in the White House meetings this summer argued for a broader reassessment. "The question is, 'Is it even worth doing now? We've got the key leadership in al Qaeda, what is it that we're there for now?" one of the officials recalled some advisers asking.

The White House review culminated in a Situation Room meeting with Mr. Obama in June in which he reaffirmed support for the program.

But changes were made. Mr. Obama instituted an appeals procedure to give the State Department more of a voice in deciding when and if to strike. If the U.S. ambassador to Pakistan objected to a strike, for example, the CIA director or his deputy would first try to talk through their differences with the ambassador. If the conflict was unresolved, the secretary of state would appeal directly to the CIA director. If they couldn't reach agreement, however, the CIA director retained the final say.

Since the changes were made, officials say internal tensions over the strikes have eased and agencies were acting more in concert with each other.

Though Mr. Petraeus voiced a preference for smaller drone strikes, officials said the agency has the leeway to carry out large-scale strikes and hasn't been formally directed to go after only higher-value targets and avoid foot soldiers. Since Mr. Petraeus's arrival at CIA, some strikes on larger groups have taken place, the senior intelligence official said.

To reduce the number of CIA strikes on Pakistani soil, the military moved more of its own drones into position on the Afghan side of the border with Pakistan, according to participants in the discussions. That makes it easier for the CIA to "hand off" suspected militants to the U.S. military once they cross into Afghanistan, rather than strike them on Pakistani soil, U.S. officials said.

U.S.-Pakistani relations remain troubled, but Islamabad recently expanded intelligence cooperation and has toned down its opposition to the drone strikes, both in public and private, officials said. Pakistani officials had sought advance notice, and greater say, over CIA strikes so they could try to mitigate the public backlash.

"It's not like they took the car keys away from the CIA," a senior official said. "There are just more people in the car."