Sen. Jack Reed (R.I.), the top Democrat on the Senate Armed Services Committee, on Wednesday upbraided Defense Secretary Mark Esper and Joint Chiefs Chairman Gen. Mark Milley about the imbalance.

“These vacancies continue to challenge the department's ability to effectively respond to national security challenges and undermine civilian input into the decision-making process with political appointees largely absent,” Reed said.

Part of the challenge of filling senior positions is that the White House personnel office, which is led by a 29-year-old Trump loyalist, is now trying to exert more control over the Pentagon’s nominating process. The two offices have not yet settled on a choice to replace John Rood, who served as the Pentagon’s top policy official until he was forced out in February, four defense and administration officials tell POLITICO.

After Rood’s ouster, Esper’s staff suggested a handful of candidates to replace him, two of the people said. But the White House personnel office was not satisfied with those options and is pushing a fourth choice: Elbridge Colby, who served as a deputy assistant secretary of Defense under former Defense Secretary Jim Mattis and is one of the primary authors of Mattis’ National Defense Strategy. He is a co-founder of the Marathon Initiative.

"DoD thinks White House is a rubber stamp, that it's Esper's position to fill and the White House is consulted as a courtesy. That may have been true in the previous PPO but that's not how John McEntee operates,” said one administration official, referring to the head of the Presidential Personnel Office. “It will be a consultation, but the White House is going to play a major, major role in selecting the replacement.”

"McEntee's going to win," the official said.

A person close to the Pentagon and Capitol Hill said the White House office "has taken total control over staffing at DoD and anything that they perceive as disloyalty is a disqualification."

"They want to make sure that there's no hint or indication of conflicting loyalties," the person said. "It's complete and total control. ... You have to be a 110 percent Trump supporter and they want nobody else. ... The problem is they're not going to identify, nominate and confirm enough people before November."

One Defense official pushed back on the notion of a disagreement between the White House and the Pentagon over Rood’s replacement.

“DoD Office of White House Liaison has shared multiple names with the White House and the White House has as well, with some overlap,” the official said. “DoD is in the process of interviewing the candidates but a decision has not been made on the finalist yet.”

The White House did not immediately respond to a request for comment. Colby could not be reached for comment.

Experts have been raising alarms over an imbalance in civilian control of the military, which has been a pillar of American democracy since the Founding Fathers wrote it into the Constitution, and since Mattis, a former general, took the reins of the Pentagon in 2017. The issue was a major focus of a 2018 congressionally-mandated report on the National Defense Strategy, the Pentagon’s guiding doctrine. Since the report came out, the problem has only worsened, Reed said.

Mara Karlin, a former Obama administration Pentagon official, acknowledged that the number of vacancies and officials serving in acting capacities “is pretty dramatic when considered historically,” though she noted that Esper “deserves credit for more actively and deliberately bringing OSD civilians to the table than either [former acting Defense Secretary Pat] Shanahan or Mattis did.”

The Pentagon's percentage of filled positions is now at 65 percent. Department spokesperson Chuck Prichard said that number was 11 percent during the transition in early 2017 and rose to 80 percent in March 2018. Traditionally, that number hovers around 70 percent, he said.

Many of the unfilled positions have been vacant for months. The role of assistant secretary of Defense for international security affairs has been filled by a temporary official since Robert Karem resigned in November 2018. Most recently, the White House withdrew the nomination for the major position of Pentagon comptroller after emails emerged showing the nominee Elaine McCusker questioning the administration’s suspension of military aid to Ukraine, an issue at the heart of the impeachment.

Reed on Wednesday pointed to the top policy position for special operations and low-intensity conflict, which has been vacant since Owen West resigned in June. In October, Reed and other lawmakers wrote Esper expressing their concern about the department’s failure to fill that position — and never received an answer.

“It’s unacceptable, frankly, that we still haven't received a response to a letter more than four months later,” Reed said.

Filling this position is of particular interest after The Washington Post reported on Thursday that the military plans to lean heavily on special operations forces to keep the Taliban and other foreign terrorist groups at bay in Afghanistan during the planned drawdown.

Esper acknowledged the difficulty of finding qualified people to fill slots in the fourth year of an administration, as well as challenges moving candidates through the nomination process. However, he maintained that the situation is not “as dire as some may think.”

“We have very capable people in the positions,” Esper said. “And we have very capable, capable DoD civilians, career civilians who also help out” — an apparent reference to the many acting officials or people wearing multiple hats. For example, James Anderson, who's been tapped for the No. 2 policy job, is also filling the top slot in an acting capacity.

Esper dismissed concerns about civilian control of the military, noting that since he took on the job he instituted a number of changes to ensure civilian voices are heard.

“The uniform and civilian leadership works together, sits together in weekly meetings. We together review our National Defense Strategy implementation,” Esper told lawmakers. “We have a much better integration today between civilians and military than we did I think nine months ago in regard to the nominations that have come out to us.”

