WASHINGTON — On a trip to Afghanistan during President Barack Obama's first term, Defense Secretary Robert Gates was stunned to find a telephone line at the military's special operations headquarters that linked directly back to a top White House national security official.
"I had them tear it out while I was standing there," Gates said earlier this month as he recounted his discovery. "I told the commanders, 'If you get a call from the White House, you tell them to go to hell and call me.'"
To Gates, the phone in Kabul came to symbolize Obama's efforts to micromanage the Pentagon and centralize decision-making in the White House. That criticism later would be echoed publicly and pointedly by Gates' successor, Leon Panetta.
The president's third Pentagon chief, Chuck Hagel, was picked partly because he was thought to be more deferential to Obama's close circle of White House advisers. But over time, Hagel also grew frustrated with what he saw as the West Wing's insularity.
There have been similar gripes from other Cabinet officials, but the friction between the White House and the Pentagon has been particularly pronounced during Obama's six years in office. That dynamic already appears to be affecting the president's ability to find a replacement for Hagel, who resigned Monday under pressure from Obama.
Within hours, former Pentagon official Michele Flournoy called Obama to take herself out of consideration, even though she was widely seen as his top choice and would have been the first woman to hold the post.
Flournoy officially cited family concerns, but people close to her say she also had reservations about being restrained like Hagel and would perhaps wait to see if she could get the job if another Democrat — namely Hillary Rodham Clinton — won the presidency in 2016.
Obama's eventual nominee will join a national security team that is under intense criticism for its response to the rise of the Islamic State group in Syria and Iraq. The president has authorized airstrikes in both countries and sent about 3,000 U.S. troops to train and assist Iraqi security forces.
He has resisted sending American troops into ground combat and has insisted the military campaign is not designed to oust Syrian President Bashar Assad, whose 3½ year assault on civilians helped create the chaos that allowed the Islamic State to thrive.
The foreign policy landscape looks far different from what Obama envisioned when he ran for the White House and pledged to end the wars in Iraq and Afghanistan.
Obama has been seen in the Pentagon as being overly suspicious of the military and its inclination to use force to address problems. To some in the Pentagon, the president's approach to the military seems particularly cool and detached when compared with that of his predecessor, Republican George W. Bush, who was more eager to embrace the military and accept its judgments.
Stephen Biddle, an occasional adviser to U.S. combat commanders, said the White House has fallen victim to "group think" and is distrustful of advice or perspectives that challenge its own.
"That's a bad policy development design," said Biddle, a political science professor at George Washington University's Elliott School of International Affairs.
Several White House, defense and other administration officials discussed the relationship between the president and the Pentagon on condition of anonymity because they were not authorized to do so publicly.
On foreign policy decision-making, Obama relies in particular on national security adviser Susan Rice and chief of staff Denis McDonough. Secretary of State John Kerry has managed to carve out some areas of influence, particularly on Iranian nuclear negotiations. Some Pentagon officials say they have seen an increasingly close relationship between Obama and Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff.
But at the Pentagon, senior officials say there is growing frustration with a lack of policy direction and clarity from the White House that has hampered the military's ability to quickly respond to fast-moving events around the world. Policy recommendations from the Pentagon are often discussed exhaustively in White House meetings that can bog down, delaying decisions and sometimes resulting in conclusions that remain vague.
Over the past year, officials said the Pentagon leadership was particularly baffled by the White House's slow deliberations on Russia's moves against Ukraine and the rise of Islamic State militants.
Earlier this fall, officials said, Hagel sent Rice a memo on Syria reflecting the views of military commanders who feel Obama's strategy lacks cohesion and has included too many one-off decisions, such as resupplying Kurdish forces fighting the militants in the Syrian town of Kobani. Hagel and military commanders were particularly concerned about a lack of clarity over Obama's position toward Assad.
On Ukraine, officials say Hagel pressed the White House to speed up the protracted debate over providing even nonlethal assistance to Ukrainian forces and to look for new options when the support the administration did provide proved ineffective in stopping Russian-backed rebels.
Obama's advisers deny Hagel was ousted because he challenged the president. They cast the former Republican senator as the wrong fit for a job in which he never appeared comfortable. The aides also defended the White House's lengthy internal deliberations, saying Obama's decision-making process reflects the complexity of the problems.
Hagel's ouster has spurred a flurry of suggestions from foreign policy experts for how Obama can repair his relationship with the Pentagon, from ousting his West Wing aides to revamping the White House's National Security Council, which has ballooned from a few dozen staffers in the 1970s to more than 400.
But Gates, the former Pentagon chief who voiced his frustrations during a forum this month at the Ronald Reagan presidential library in California, suggested the real issue rested with the president himself.
"When a president wants highly centralized control in the White House at the degree of micromanagement that I'm describing, that's not bureaucratic, that's political," he said.