WASHINGTON >> President Barack Obama’s decision to send an intelligence chief to the Pentagon and a four-star general to the Central Intelligence Agency is the latest evidence of a significant shift over the past decade in how the United States fights its battles — the blurring of lines between soldiers and spies in secret U.S. missions abroad.

On Thursday, Obama is expected to announce that Leon Panetta, the CIA director, will become secretary of defense, replacing Robert Gates, and that Gen. David Petraeus will return from Afghanistan to take Panetta’s job at the CIA, a move that is likely to continue this trend.

As CIA director, Panetta hastened the transformation of the spy agency into a paramilitary organization, overseeing a sharp escalation of the CIA’s bombing campaign in Pakistan using armed drone aircraft, and an increase in the number of secret bases and covert operatives in remote parts of Afghanistan. 

Petraeus, meanwhile, has aggressively pushed the military deeper into the CIA’s turf, using Special Operations troops and private security contractors to conduct secret intelligence missions. As commander of the U.S. Central Command in September 2009, he also signed a classified order authorizing U.S. Special Operations troops to collect intelligence in Saudi Arabia, Jordan, Iran and other places outside of traditional war zones.

The result is that U.S. military and intelligence operatives are at times virtually indistinguishable from each other as they carry out classified operations in the Middle East and Central Asia. Some members of Congress have complained that this new way of war allows for scant debate about the scope and scale of military operations. In fact, the U.S. spy and military agencies operate in such secrecy now that it is often hard to come by specific information about the U.S. role in major missions in Iraq, Afghanistan, Pakistan and now Libya and Yemen.

The operations have also created tension with important allies like Pakistan, while raising fresh questions about whether spies and soldiers deserve the same legal protections.  

Officials acknowledge the lines between soldiering and spying have blurred.

“It’s really irrelevant whether you call it a covert action or a military special operation,” said Dennis Blair, a retired four-star admiral and a former director of national intelligence. “I don’t really think there is any distinction.”

The phenomenon of the CIA becoming more like the Pentagon, and vice versa, has critics inside both organizations. Some inside the CIA’s clandestine service believe that its bombing campaign in Pakistan, which has become a cornerstone of the Obama administration’s counterterrorism strategy, has distorted the agency’s historic mission as a civilian espionage agency and turned it into an arm of the Defense Department.

Henry Crumpton, a career CIA officer and formerly the State Department’s top counterterrorism official, praised Petraeus as “one of the most sophisticated consumers of intelligence.” But Crumpton warned more broadly of the “militarization of intelligence” as current or former uniformed officers assume senior jobs in the sprawling U.S. intelligence apparatus. 

For example, James R. Clapper Jr., a retired Air Force general, is director of national intelligence, Obama’s top intelligence adviser. Maj. Gen. Michael Flynn, formerly the senior intelligence officer in Afghanistan, is soon expected to become of one of Clapper’s top deputies.

“If the intelligence community is populated by military officers, they understandably are going to reflect their experiences,” Crumpton said.

At the Pentagon, the new roles raise legal concerns. The more that soldiers are used for espionage operations overseas, the more they are at risk of being thrown in jail and denied Geneva Convention protections if they are captured by hostile governments.

And yet few believe that the trend is likely to be reversed. A succession of wars has strained the ranks of both the Pentagon and the CIA, and the United States has come to believe that many of its current enemies are best fought with timely intelligence rather than overwhelming military firepower.  

These factors have pushed military and intelligence operatives more closely together in the years since the attacks of Sept. 11, 2001.

“In the field, there is a blurring of the mission,” said Sen. Jack Reed, a senior Rhode Island Democrat on the Armed Services Committee who served as an officer in the 82nd Airborne Division. “Military operations can buy time to build up local security forces, but intelligence is the key to operations and for anticipating your adversary.”

U.S. officials said that, for the most part, the tensions and resentments were greatly reduced from the days when Defense Secretary Donald Rumsfeld expanded Pentagon intelligence-gathering operations to become less dependent on the CIA.

The secret “Execute Order” signed by Petraeus in September 2009 authorized U.S. Special Operations troops to carry out reconnaissance missions and build up intelligence networks throughout the Middle East and Central Asia in order to “penetrate, disrupt, defeat and destroy” militant groups and “prepare the environment” for future U.S. military attacks. But that order greatly expanding the role of the military in spying was drafted in consultation with the CIA, administration officials said.

Petraeus has worked closely with the CIA since the Bosnia mission in the 1990s, a relationship that grew during his command tours in Iraq and Afghanistan. In fact, some of the missions he has overseen seem to have been more like clandestine operations than traditional military missions.

Even before Petraeus took over as the leader of the military’s Central Command overseeing Middle East operations nearly three years ago, he ordered a study of the threat posed by militants in a country few U.S. policy makers had focused on — Yemen. Al-Qaida’s branch in Yemen is now considered the most immediate threat to the United States

The general’s relationship with Yemen’s mercurial president, Ali Abdullah Saleh, was well documented in the diplomatic cables released by WikiLeaks last year. And the military’s operations there, beginning with airstrikes in December 2009, are shrouded in even more secrecy than the CIA’s drone attacks in Pakistan. 

Saleh, however, drew the line at Petraeus’ request to send U.S. advisers to accompany Yemeni troops on counterterrorism operations.

Now, with Saleh’s government teetering on the verge of collapse, Petraeus is taking over at the CIA — and will once again be part of America’s secret war in Yemen.

© 2011 The New York Times Company