Firing Attorney General Jeff Sessions, as President Trump has repeatedly hinted he might do, would leave key components of the Justice Department in the hands of the very career officials the president has railed against as his “deep state” enemies.

Mr. Trump has yet to win confirmation — or in many cases even to nominate — people for 18 key posts, including the head of the civil rights division and the chief of the Drug Enforcement Administration, leaving many of those jobs performed by senior career officials who may, or may not be, on the same page as the Trump White House.

“If you don’t have confirmed political appointees in these positions, it’s tough for the president’s priorities to get accomplished,” said Hans von Spakovsky, a former Justice Department official who is now a legal fellow at the conservative Heritage Foundation. “There are some very good interim guys in there, but they don’t have the final stamp of approval that a confirmed individual does, and they may hesitate to take some of the steps necessary because it may cause problems for a nominee waiting to be confirmed.”

The Justice Department has 15 positions that require confirmation but for which nobody has been nominated, and another three with nominees waiting for action on Capitol Hill, according to the Partnership for Public Service, a nonpartisan research group in Washington. The Justice Department lags behind only the State Department, which has 130 openings, and Defense and Treasury, with 22 apiece.

Analysts say vacancies can hinder a president’s agenda at any time, leaving agencies and divisions without clear direction.

But the Justice Department vacancies could be a particular problem for Mr. Trump, who has repeatedly complained about left-leaning employees at the department — though he is also upset about the performance of his attorney general, Mr. Sessions.

Should the president fire Mr. Sessions — which the White House has signaled wouldn’t happen until after the November elections — he likely also would oust Deputy Attorney General Rod Rosenstein.

That normally would leave the department in the hands of the associate attorney general — but that position has been empty since Rachel Brand, a conservative superstar, resigned in February.

“The Trump White House has seen more turnover in top jobs than any other administration we’ve seen,” said Max Stier, president and CEO of the Partnership for Public Service. “That turnover is problematic because it’s hard enough to fill the job once, and they are not doing a great job at that, but to fill it twice is a real problem.”

As it stands, the next in line would be Solicitor General Noel Francisco, another conservative star. But his serving as acting attorney general would bring its own problems, analysts said.

Mr. Francisco, a Trump appointee, has been mum about special counsel Robert Mueller’s Russia investigation, but he has been skeptical about political corruption investigations, suggesting they have overreached. He also accused former FBI Director James B. Comey of using “kid gloves” in the investigation into Hillary Clinton’s use of a secret email server while secretary of state.

Those statements could create the appearance of bias if he is suddenly put in charge of Mr. Mueller’s investigation into the 2016 presidential election.

“If Sessions is gone and the deputy attorney general is gone and no one is in the third spot, it’s going to be a mess,” said Rory Little, a former Justice Department lawyer who is now a professor at the University of California’s Hastings College of the Law.

Under more normal circumstances, the president could have names ready to fill empty slots.

But Mr. Trump’s antipathy toward the Mueller investigation, stacked up against senators’ insistence that the probe be allowed to run its course, makes the situation anything but normal.

“A replacement is going to be put in the position of being ordered by the president to end the Mueller investigation, which will be terrible for their reputation, or refusing to do it and being removed as a result,” said Julian Sanchez, a senior fellow at the Cato Institute. “That’s not an attractive position to be in — especially if you are the kind of person whose career has been aimed at a high-ranking legal role in a Republican administration.”

Even if someone accepts the nomination, the confirmation process could be even more bitter than the one for Supreme Court nominee Brett M. Kavanaugh.

“The combination of getting rid of Sessions, who many of the folks in the Senate have a great deal of respect for, for a replacement who is willing to do what Trump wants on the Russia inquiry is not the kind of person who would sail through,” Mr. Sanchez said.

The administration gave up on trying to fill the associate attorney general’s position after several potential candidates said they weren’t interested, according to a report in The Wall Street Journal.

Mr. von Spakovsky said the White House needs to start filling some of the other agency and division head positions, and that means gearing up for a series of confirmation battles.

“The Democrats have been preventing some of these appointments because they know the vast majority of career people in the Justice Department divisions are big liberals and big Democrat supporters,” he said. “I worked there in the [George W.] Bush administration, and we were constantly having internal battles with senior career people who wanted to threaten everything Bush wanted to do. Trump has the same problem.”

It has taken 89 days on average for Mr. Trump’s Justice Department candidates to receive confirmation. That compares with 83 days for President Obama, 53 days for President George W. Bush and 65 days for President Clinton.

Lawmakers aren’t the only source of delay.

Of the 18 vacant confirmable positions in the Justice Department, the administration hasn’t named picks for 15.

“We are over 18 months into this administration, and the reality is that getting people confirmed between now and after the midterms when Congress has a lot of other things they are working on and won’t be much longer is going to be near impossible,” Mr. Stier said. “If you don’t go quickly at the start of your administration, it just becomes harder and harder.”

Others say Mr. Sessions needs to push harder to get the positions filled. But as the relationship between Mr. Trump and his attorney general becomes more frayed, it is not clear whether the White House would listen to him.

When Ronald Reagan was elected in 1980, he made it a priority to have all open Justice Department positions filled by June 1981, said former Attorney General Edwin Meese III, who held the title during Reagan’s second term.

“I didn’t want any of those positions vacant for any period of time at all,” he said. “When I came in, there were several vacancies because it was when the administration had moved from the first to the second term. We worked to fill those very quickly.”

Mr. Meese said it helps to have a person within the Justice Department champion nominees. For example, John R. Bolton, who was the department’s assistant attorney general for legislative affairs under Mr. Meese and is now Mr. Trump’s national security adviser, filled that role in the Reagan administration. In other administrations, the deputy attorney general handled that job, Mr. Little said.

But no one is available to take the reins in the Trump administration because of the fractured relationship between the president and the top two positions at Justice.

“We’ve never had a situation where you did not have at least a reasonable agreement between the president and the attorney general and the deputy attorney general,” Mr. Meese said.

Mr. von Spakovsky said the number of vacancies is likely to rise given that presidential appointees usually serve for only a year and a half or so.

“We are going to start to see turnover in the confirmed slots, and the patience is going to run out for the people who have been nominated for a year and a half but haven’t been confirmed. We could need a whole new slate, and who knows how long it will take to get those folks confirmed?” he said.

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