WASHINGTON — The Justice Department said Tuesday it will take the extraordinary step of lowering the amount of prison time it will seek for Roger Stone, an announcement that came just hours after President Donald Trump complained that the recommended sentence for his longtime ally and confidant was “very horrible and unfai r.”

The Justice Department said the decision to shorten the sentencing recommendation was made Monday night — before Trump’s tweet — and that prosecutors had not spoken to the White House about it.

But the move was sure to raise questions about political interference and whether Trump’s views hold unusual sway over the Justice Department, which is meant to operate independently of the White House in criminal investigations and prosecutions.

Attorney General William Barr has been a steady ally of Trump’s, clearing the president of obstruction of justice even when special counsel Robert Mueller had pointedly declined to do so and declaring that the FBI’s Russia investigation — which resulted in charges against Stone — had been based on a “bogus narrative.”

On Monday night, prosecutors had recommended Stone serve seven to nine years behind bars after being convicted of charges including lying to Congress, witness tampering and obstructing the House investigation into whether the Trump campaign coordinated with Russia to tip the 2016 election. The recommendation raised the prospect that Stone could receive the harshest sentence of any of the half-dozen Trump aides charged in Mueller’s probe.

In a tweet early Tuesday, Trump said the case against Stone was a “miscarriage of justice.” A Justice Department official said authorities decided to step in and seek a shorter sentence because they had been taken by surprise by the initial recommendation. The person, who spoke on condition of anonymity, said prosecutors had told the department to expect a shorter recommendation.

It is extremely rare for Justice Department leaders to reverse the decision of its own prosecutors on a sentencing recommendation, particularly after that recommendation has been submitted to the court. Normally, United States attorneys have wide latitude to recommend sentences on cases that they prosecuted.

Sentencing decisions are ultimately up to the judge, who in this case may side with the original Justice Department recommendation. U.S. District Judge Amy Berman Jackson has repeatedly scolded Stone for his out-of-court behavior, which included a social media post he made of the judge with what appeared to be crosshairs of a gun.

The judge barred Stone from social media last July after concluding that she repeatedly flouted his gag order.

Besides, judges invariably frown upon crimes that they see as perverting the functions of the criminal justice system, such as making false statements or obstructing an investigation.

The Justice Department plans to refile the recommendation later Tuesday.

Federal prosecutors also recently softened their sentencing position on former national security adviser Michael Flynn, saying that they would not oppose a probation of punishment after initially saying that he deserved up to six months in prison for lying to the FBI. The Flynn prosecution is also being handled by the U.S. Attorney’s office in Washington.

The White House referred questions about the decision to the Justice Department.

In the sentencing memorandum filed Monday evening, prosecutors asked for Stone to serve between 87 and 108 months in federal prison — the sentence they said was in line with federal guidelines. Such a sentence would send a message to deter others who might consider lying or obstructing a congressional probe or tampering with witnesses, they said.

The prosecutors wrote in the court papers that “Stone’s actions were not a one-off mistake in judgement” and that he “decided to double – and triple – down on his criminal conduct by tampering with a witness for months in order to make sure his obstruction would be successful.”

Stone has denied wrongdoing and consistently criticized the case against him as politically motivated. He did not take the stand during his trial and his lawyers did not call any witnesses in his defense.

Witnesses in the case testified that Trump’s campaign viewed Stone as an “access point” to the anti-secrecy site WikiLeaks, which was in possession of more than 19,000 emails hacked from the servers of the Democratic National Committee and tried to use him to get advance word about hacked emails damaging to Hillary Clinton.

Prosecutors charged that Stone lied to Congress about his conversations about WikiLeaks with New York radio host Randy Credico — who had scored an interview with WikiLeaks founder Julian Assange in 2016 — and conservative writer and conspiracy theorist Jerome Corsi.

During the 2016 campaign, Stone mentioned in interviews and public appearances that he was in contact with Assange through a trusted intermediary and hinted at inside knowledge of WikiLeaks’ plans. But he started pressing Credico to broker a contact, and Credico testified that he told Stone to work through his own intermediary.

Earlier testimony revealed that Stone, while appearing before the House Intelligence Committee, named Credico as his intermediary to Assange and pressured Credico not to contradict him.

After Credico was contacted by Congress, he reached out to Stone, who told him he should “stonewall it” and “plead the fifth,” he testified. Credico also testified during Stone’s trial that Stone repeatedly told him to “do a ‘Frank Pentangeli,’” a reference to a character in “The Godfather: Part II” who lies before Congress.

Prosecutors also charged that Stone had threatened Credico’s therapy dog, Bianca, saying he was “going to take that dog away from you.”