President Obama has picked CIA Director Leon E. Panetta to replace holdover Defense Secretary Robert M. Gates in the next two months and will move the top Afghanistan War commander, Gen. David H. Petraeus, to take the senior intelligence post in a major shift of national security aides.
The nominations are part of a larger shuffle of the president’s war cabinet as he gears up for the 2012 election.
The changes will bring new officials to the top positions in the U.S. military as the United States grapples with three low-level wars, including a replacement for Adm. Mike Mullen, chairman of the Joint Chiefs of Staff.
The decision to replace Mr. Gates - who took over the top Pentagon slot after the 2006 elections when Democrats regained control of Congress - shows Mr. Obama is looking for a closer ally to lead the Pentagon, although Mr. Gates reportedly lobbied for Mr. Panetta, a centrist Democrat, to be his replacement.
Mr. Panetta has worked quietly at the CIA with the difficult task of working with Pakistan’s powerful intelligence service in supporting the agency’s covert role in the war on terrorism in Southwest Asia, which has included large-scale use of armed drone aircraft attacks on al Qaeda.
He became a trusted adviser to Mr. Obama and made numerous visits to Pakistan to manage the fraying intelligence relationship with Islamabad.
Mr. Gates made known his desire to step down several months ago and recently made public his opposition to U.S. involvement in the air war over Libya during congressional testimony. The testimony was given as the White House sought to build political support for what it has called a humanitarian intervention.
Mr. Gates also has stated that he opposes deeper budget cuts by the administration in defense spending than those he announced earlier this year.
“The sum total of these picks is that the president has chosen experienced people with unique capabilities to serve our nation at a dangerous time,” Sen. Lindsey Graham, South Carolina Republican, said in a key Republican endorsement. “I could not be more pleased with these selections.”
The appointment of a second intelligence chief to head the Pentagon - Mr. Gates is a former CIA director - also is a sign that the president is continuing to emphasize intelligence operations and covert action over conventional military activities in the global war on terrorism since the attacks of Sept. 11, 2001.
Mr. Gates tenure at the Pentagon was marked by efforts to shift the strategic focus of the military from waging major conventional wars to counterinsurgency and counterterrorism. In doing so, he clashed with senior military leaders and ended up firing several senior generals and senior defense officials.
Sending a wartime commander, Gen. Petraeus, to head the CIA also highlights the closer links between military and intelligence operations in the war against terrorism.
“Putting a military guy in charge of the agency is as effective as putting an intelligence guy in charge of the Department of Defense,” said Rick Nelson, a senior fellow at the Center for Strategic and International Studies.
“They work so closely together, it is important to forge that relationship through this kind of appointment. They are dependent on each other.”
Former Sen. Christopher S. Bond, who served as vice chairman of the Senate Select Committee on Intelligence until December, said he was pleased with both selections.
“Petraeus as a user of intelligence would bring a great sense of how the agency can better help the war fighters,” the Missouri Republican said. “I also hope he understands, and I am sure he does, the broader mission of the agency, to serve the policymakers, where the military may not be directly involved.”
Sen. Dianne Feinstein, California Democrat and chairwoman of the Senate intelligence panel, said she looked forward to hearing Gen. Petraeus’ vision for the agency.
“He is clearly a very accomplished officer and familiar with the parts of the world where many of the threats to our security originate,” she said. “But that is a different role than leading the top civilian intelligence agency. I look forward to hearing his vision for the CIA and his plans to make sure the CIA is collecting the type of intelligence that policymakers need.”
Louis Tucker, who served as the minority staff director on the Senate intelligence panel until January, said Mr. Panetta was a good choice for the Pentagon, which still controls most of the execution authority of the $80 billion annual intelligence budget for the 16 civilian and military agencies.
“This pick is a little surprising,” said Mr. Tucker. “I thought Panetta was well placed at the agency and doing a great job. He is one of the best in the administration we have at the senior level of the government in national security and defense, so I am sure he will do a good job at the Pentagon.”
Mr. Panetta’s record at the CIA is mixed. He is leaving the job with the strategic U.S.-Pakistani intelligence relationship severely strained. At the same time, he oversaw a drone war in Pakistan that the CIA has said has killed or forced into hiding senior al Qaeda leaders.
During Mr. Panetta’s tenure, the CIA also discovered a clandestine nuclear facility in Iran outside of Qom.
Mr. Panetta prevailed over Mr. Obama’s first director of national intelligence, Dennis C. Blair, in a bureaucratic battle over the top intelligence representative at U.S. embassies. That person will remain the CIA station chief and not a separate representative of the Office of the Director of National Intelligence as Mr. Blair had wanted.
Gen. Petraeus, commander of the International Security Assistance Force in Afghanistan, has had a mixed relationship with the CIA over the years. After he took charge of Multi-National Forces Iraq, Gen. Petraeus asserted his authority as combat commander to be briefed on and approve all CIA activities in Iraq.
One former senior U.S. intelligence official said, however, that in Iraq, Gen. Petraeus was grateful for the CIA’s work in uncovering the supply chain to Iran of deadly improvised explosives that were the major killers of U.S. forces in the country at the time.
In Afghanistan, Gen. Petraeus clashed with the CIA over the mission of the war. The four-star general supported a counterinsurgency strategy that relied on the establishment of credible and trusted local and provincial government institutions as a way to win support of the population from elements of the Taliban.
The CIA - which since Sept. 11 has cultivated relationships with many warlords, such as Afghan President Hamid Karzai’s brother, Ahmad Wali Karzai - favored a counterterrorism strategy that relied on good relations with those warlords.
The tensions between Gen. Petraeus and the agency in Afghanistan, however, have been muted in recent months, said two U.S. military officials who asked not be quoted by name.
“David Petraeus came to understand how the CIA could work closely with special forces in Afghanistan. That combination has become one of the main hammers in the war today,” one such military official said.
The White House is expected to make the announcement on Thursday. Mr. Panetta, pending confirmation, is scheduled to take over the Pentagon by July. Gen. Petraeus is expected to assume his position at the CIA in September.