The CIA three months ago suspended its long-standing use of an air base in Pakistan as a launch site for armed drones targeting members of al-Qaeda and other militant groups, according to U.S. and Pakistani officials.

U.S. personnel and Predator drones remain at the facility, in the southwestern province of Baluchistan, with security provided by the Pakistani military, officials from both countries said. In recent days, Pakistan has publicly declared that it “ended” all U.S. flights from the base in the wake of the secret U.S. commando raid that killed al-Qaeda leader Osama bin Laden in May.

But U.S. and Pakistani officials said the aircraft launches were halted in April, weeks before the bin Laden raid, after a dispute over a CIA contractor who fatally shot two Pakistani citizens in Lahore in January. An American official said the CIA’s decision to suspend the launches was part of a U.S. effort to “pay attention to the sensitivities” of the Pakistanis, who had objected to a claim of diplomatic immunity for the contractor.

Although Pakistan has continued to voice sharp public criticism over the shootings and the bin Laden raid, officials from both countries said the rupture in their intelligence cooperation has slowly begun to heal. Pakistan has reversed its freeze on visas for U.S. intelligence officials, they said, and allowed dozens of CIA personnel to reenter the country.

All U.S. drone strikes in the past three months have been launched from Afghanistan, in the vicinity of Jalalabad, according to the officials, who spoke about intelligence matters only on the condition of anonymity. The New America Foundation, which tracks the strikes, has listed 23 such raids since the beginning of April, all but one in Pakistan’s tribal regions of North and South Waziristan. A June 20 attack was reported in Kurram, an area above North Waziristan along the Afghanistan border.

The drone program has become increasingly controversial as the Obama administration has expanded its use beyond the Afghanistan and Iraq wars. Lethal missiles have been launched from unmanned aircraft in at least five countries in addition to Pakistan — Afghanistan, Iraq, Libya, Yemen and, most recently, Somalia. The military’s Joint Special Operations Command last week used a drone to attack what officials said were two senior members of the al-Shabab militant group near Kismaayo, on the southern Somali coast.

A U.S. official said Friday that the two “killed last week in Somalia were looking to conduct attacks in Europe” and that the specific target was Britain, but declined to provide details indicating the imminence or specifics of any plans. Some initial reports indicated that the two militants had been wounded but not killed.

Some international law experts and human rights groups have questioned the expanded use of drones and the legality of such strikes in countries with which the United States is not at war. In Libya, where the Defense Department said 42 drone strikes have been launched by U.S. Predator aircraft as of Tuesday, the United States is operating under NATO command in a U.N.-authorized mission.

In other cases, the administration has cited international laws of self-defense and the 2001 congressional authorization to strike the al-Qaeda perpetrators of the Sept. 11 attacks that year. John O. Brennan, who this week unveiled the administration’s new national counterterrorism strategy, said the United States was “at war” with al-Qaeda and named al-Shabab and Yemen-based al-Qaeda in the Arabian Peninsula as among its affiliates.

Some critics have also raised questions of morality and said the drone program goes beyond the commonly accepted standards of warfare, because the “pilots” direct the aircraft remotely, often from half a world away in the comfort of secure facilities. The administration and defenders of the aircraft have countered that the weapons prevent U.S. military combat fatalities and that their precision greatly limits civilian casualties.

Brennan, in response to questions after his counterterrorism speech this week at the Johns Hopkins School of Advanced International Studies, said that for “nearly the past year, there hasn’t been a single collateral death, because of the exceptional precision” of such strikes. According to the New America Foundation, since April, drone-fired missiles have killed 133 to 191 militants in Pakistan and up to 10 civilians.

Predator targeting choices and collateral deaths have long been a subject of dispute between the United States and Pakistan, where public opinion is vehemently opposed to the strikes. The Pakistanis charge that the Americans use the weapons indiscriminately against militant “foot soldiers” rather than concentrating on top commanders, and residents in the tribal regions have cited civilian deaths.

Brennan indicated that such “surgical” strikes were increasingly the administration’s weapon of choice in the fight against al-Qaeda.

Nowhere has the weapon proved more effective than in Pakistan, where al-Qaeda, the Taliban and other militant organizations maintain their headquarters and training camps, but where U.S. ground troops are prohibited.

Former Pakistani president Pervez Musharraf secretly authorized the CIA, under the George W. Bush administration, to operate drones from Shamsi, a small air facility in Baluchistan.The air strip, located about 600 miles southwest of Islamabad, apparently was constructed years ago by the ruling family of the United Arab Emirates as an arrival point for falconry and other hunting expeditions in Pakistan.
A May 2005 State Department cable from the U.S. Embassy in the UAE reported that government’s displeasure that news of the arrangement, and use of the airfield, was revealed in a book published by retired Gen. Tommy Franks, the former head of the U.S. Central Command.

Although established U.S. air bases in Afghanistan are arguably closer to the tribal areas across the border in Pakistan, the United States was pleased at Pakistan’s involvement in the operation, even as a silent partner. The number of CIA personnel, along with contractors from the private security company then known as Blackwater, grew as the Obama administration rapidly increased the number of drone strikes.

In the weeks immediately after Pakistan’s grudging release in March of the CIA contractor involved in the Lahore shooting, top Pakistani military and intelligence officials made “a formal, personal request . . . a demand . . . more than once” to their U.S. counterparts to end the flights and leave Pakistan, a senior Pakistani defense official said.

In response, the official said, “there has been some thinning out at the base, and the drone missions suspended.”

Staff researcher Julie Tate contributed to this report.