Pakistan appointed a new head of intelligence on Friday, injecting some uncertainty in America's dealings with an agency crucial to its hopes of negotiating a peace deal with the Afghan Taliban and keeping pressure on al-Qaida.
Lt. Gen. Zaheerul Islam replaces Lt. Gen. Ahmad Shuja Pasha, who had been in the post since 2008 and was due to retire on March 18. The scion of a military family who is currently army commander in the city of Karachi, Islam was considered a likely man for the job.
Islam, who between 2008 and 2010 was the deputy head of the powerful Inter-Services Intelligence, will be a major player in any Pakistani efforts to get the Afghan Taliban to enter peace negotiations to end the war. ISI agents helped build up the Afghan Taliban in the 1990s, and its leaders are believed to be based in Pakistan. The ISI is considered to have some influence over them.
While there remain doubts over its loyalty, the ISI also works closely with the CIA in tracking and capturing members of al-Qaida, which retains a global command and training center close to the Afghan border.
Relations between Islamabad and the United States have been strained since the U.S. raid that killed Osama bin Laden last year and have all but collapsed since November, when American troops mistakenly killed 24 Pakistani troops on the Afghan border. Intelligence cooperation between them has continued despite the tensions, officials from both nations have said.
The ISI falls under the control of the army, which sets policy in consultation with the elected government.
As such, the appointment of Islam is not expected to immediately, or significantly, change Pakistani policy, but having a new man at the helm inevitably brings a measure of uncertainty in American dealings with the spy agency. The current head of the army, Gen. Ashfaq Pervez Kayani, is due to retire in October 2013.
"There is now a variable. Except for his close relations, who knows what he believes in? When he comes under stress, how will he react?" said Moeed Pirzada, a political commentator.
A U.S. official said Islam had traveled to America during his career to attend U.S. military sponsored training programs, and was familiar with his American counterparts.
"It would not be a surprise to see a brief transition period as the new head of the ISI gets up to speed, but that shouldn't have much impact on counter terrorism cooperation," said the official, speaking anonymously to talk about intelligence matters.
Islam has also served as head of the ISI's internal security wing, which deals with militants and counterintelligence. As army chief in Karachi, he would have intimate knowledge of the militant groups in the city, which has been frequently hit by terrorist attacks since 2001.
Pasha headed the spy service during a tumultuous time, especially after the bin Laden raid in May.
Abroad, bin Laden's presence in the military town of Abbottabad only heightened suspicions that elements of the ISI may have been protecting him. At home, the military establishment was criticized for failing to track him down, as well as not preventing the unilateral American airborne raid.
Shuja Nawaz, the director of the South Asia Center at the U.S.-based Atlantic Council, said the change of ISI chief "wouldn't makes a great deal of difference" in Pakistani policy.
"Instructions will continue to come from the army chief. However, there are always the personal likes and dislikes of the individual who takes over the ISI because the army chief is not supervising every micro detail," he said, speaking before Islam's appointment was announced.
Militants attacked ISI offices several times over the last four years, and Pasha had to ramp up the agency's fight against them. During his tenure, the CIA dramatically expanded its drone strike program against militants along the Afghan border, allegedly with the support of the ISI.
Earlier Friday, an American missile attack killed 12 militants in South Waziristan, a rugged militant stronghold where the Pakistani army has staged offensives in the past, intelligence officials said. The attack was the eighth this year, which represents a drop in frequency over the past two years. In 2011, there were an average of two strikes a week.
The strikes, which began in earnest in 2008, have killed scores of militants, including foreign al-Qaida members involved in plotting attacks on the West. Their tempo increased in 2010, when they hit militants widely seen as being proxies of the Pakistani army, causing friction between the U.S and Pakistan.
Also Friday, an al-Qaida video released on the Internet confirmed the death of militant commander Badr Mansoor in a missile attack in February. Mansoor was believed to be behind many of the suicide attacks inside Pakistan in recent years, and so his death could be cited by supporters of the campaign in Washington and Islamabad as an example of how drone attacks benefit both countries.
Mansoor was from Pakistan's largest province, Punjab, and moved to North Waziristan in 2008, where he led a faction of some 230 fighters, local insurgents have said. The enlistment of Punjabis in the Pakistani Taliban has been a serious concern for the government, because it makes it easier for the militants to export violence from the border to the heart of the country, where most Punjabis live.
Associated Press writers Ishtiaq Mahsud in Dera Ismail Khan, Pakistan, Sebastian Abbot in Afghanistan and Kimberly Dozier in Washington contributed to this report.
(This version corrects to relations between Islamabad and the United States in fifth paragraph.)