Sen. Jeff Sessions (R-Ala.) appears at a campaign event with Donald Trump in Alabama in February. As president-elect, Trump has nominated Sessions to be attorney general. (John Bazemore/AP)

The Justice Department has long enjoyed a measure of ­independence in the executive branch, even though its boss is appointed by, and answers to, the president. The president sets a broad policy agenda, which the Justice Department plays a role in implementing, but when it comes to a particular criminal investigation, the White House generally steers clear.

On Tuesday, President-elect Donald Trump and a senior adviser made comments that call into question that order of things. The adviser, Kellyanne Conway, suggested that Trump had indicated that he “doesn’t wish to pursue” charges against Hillary Clinton.

Although Trump later said he would not take investigations off the table, he asserted that his preference would be to move on.

“My inclination would be for whatever power I have on the matter is to say, let’s go forward,” Trump told the New York Times, seeming to suggest that he did not favor prosecution of Clinton-related cases. “This has been looked at for so long, ad nauseam.”

President-elect Donald Trump's supporters often chanted "lock her up" when he discussed his opponent, Hillary Clinton, at campaign rallies. But despite repeatedly promising to appoint a special prosecutor to investigate her, it looks like Trump might not pursue Clinton after all. (Peter Stevenson/The Washington Post)

Trump had vowed during the campaign to appoint a special prosecutor to look at Clinton’s use of a private email server while she was secretary of state, and he remarked that, were he president, Clinton would “be in jail.” He seemed to back down, at least somewhat, from that controversial promise on Tuesday, and legal analysts said he did so in a way that demonstrates a misunderstanding of what role he should play in Justice Department investigations.

“Trump’s implicit assumption that he can direct the Department of Justice to prosecute Clinton — or not — demonstrates a dangerous assumption the president can dictate the department’s prosecutorial decisions,” said Jennifer Daskal, an associate professor of law at American University and former senior Justice Department official. “But the Department of Justice depends on its independence as the source of its authority and power.”

Even Sen. Jeff Sessions (R-Ala.), the president-elect’s pick for attorney general, has long advocated for the Justice Department’s independence.

“You understand that your role is such that, on occasion, you have to say ‘no’ to the person that actually appointed you to the job and who you support?” Sessions asked current Attorney General Loretta E. Lynch during her confirmation hearing last year.

“People have agendas, and attorneys general sometimes do, and they have to guard against that and be objective,” Sessions added later.

Spokesmen for Trump and Sessions did not immediately return messages seeking comment for this article. David Kendall, an attorney for Clinton, declined to comment. Former New York mayor Rudolph W. Giuliani (R), who is considered a contender for a Cabinet post, said Tuesday that “there is a tradition in American politics that after you win an election, you sort of put things behind you, and if that’s the decision he reached, that’s perfectly consistent with the historical pattern.”

Trump could theoretically order Sessions to take particular actions, even in criminal cases. Presidents often shape the broad agenda of the Justice Department — for example, telling the attorney general to devote more resources to immigration cases. Trump also has said he had not made up his mind on whether he would ask for the resignation of FBI Director James B. Comey, who is in the middle of a 10-year term.

FBI Director James B. Comey is in the third year of his 10-year tenure, but President-elect Donald Trump won’t say if he will keep him. The Post’s Sari Horwitz explains why. (Bastien Inzaurralde/The Washington Post)

Doing that might come with significant political costs, as would making specific demands in a criminal investigation.

“The attorney general does not have legal independence from the president,” said George J. Terwilliger III, who served as deputy attorney general under President George H.W. Bush. “Politically, in almost all circumstances, it’s a lot smarter for a president to afford an attorney general independence, particularly in criminal matters, but most acutely as to specific cases.”

Trump could move to pardon Clinton, though she would have to accept to make it legally valid. That would possibly be “the most direct way to ensure that this issue goes away,” said Jacob Frenkel, a former federal prosecutor.

MSNBC first reported that Trump would not pursue investigations of Clinton both for her use of a private email server while she was secretary of state and for the financial dealings of her family’s charitable foundation, and Conway later appeared on the network and seemed to confirm the reporting.

“I think when the president-elect, who’s also the head of your party now, Joe, tells you before he’s even inaugurated he doesn’t wish to pursue these charges, it sends a very strong message, tone and content to the members,” Conway said, addressing host Joe Scarborough.

Trump himself, pressed on the issue in a meeting with New York Times reporters on Tuesday, said “no” when asked whether he would take investigations off the table for the Clintons. He also made comments suggesting that he wanted to move beyond the matter and said that a prosecution would be “very, very divisive for the country.”

Even talking about investigations can be viewed as improper meddling. Conservatives criticized President Obama for commenting while the Clinton email investigation was ongoing that Clinton had not jeopardized the United States’ national security — which some saw as subtly influencing the investigation even though the FBI and the Justice Department maintained that it was done independently.

Trump’s prior remarks about appointing a special prosecutor drew widespread criticism. But after the election, Trump did not back down. Asked on CBS’s “60 Minutes” whether he would appoint a special prosecutor, he said, “I’m going to think about it.” He later said, “She did some bad things.”

Stephen I. Vladeck, a law professor at the University of Texas at Austin, said Trump’s call for a special prosecutor reflected his lack of knowledge about the Justice Department, and Conway’s remark Tuesday reinforced it.

“The attorney general answers to the president, but the department is supposed to be independent, especially when it comes to prosecutorial decisions,” Vladeck said. “Any president, especially our next president, needs to both understand and respect that — or else they risk politicizing criminal prosecutions in ways that can be damaging.”

If Trump is now standing down from that call, that would — in some ways — reflect a return to normalcy. The FBI director said in July that “no reasonable prosecutor” would bring a case against Clinton or her aides in that investigation, and the Justice Department closed the matter without filing charges.

The Clinton Foundation investigation, though, is separate, and Trump’s involvement there would be a violation of procedure. In February, agents from the FBI’s New York field office made a pitch to career public integrity prosecutors to pursue the matter, but they were told they did not have enough evidence, people familiar with the case have said. The agents, though, kept their efforts alive, the people said.

Sessions has said it “seems like” the FBI had not fully investigated the dealings of the Clinton Foundation while Clinton was secretary of state.

There has been at least one famous instance of presidential meddling in Justice Department affairs. Richard M. Nixon ordered his attorney general and deputy attorney general to fire a special prosecutor looking into the ­Watergate break-in, and both men resigned in protest.