The revised sentencing memorandum, which is expected to be filed in Washington federal court later Tuesday, comes hours after Trump publicly criticized the recommendation, and the move will again raise questions about the Justice Department’s independence from political pressure.

Prosecutors from the US Attorney’s office in Washington, who are employees of the Justice Department, had said Monday that Stone should be sentenced to seven to nine years in prison after he was convicted on seven charges last year that derived from special counsel Robert Mueller’s investigation, including lying to Congress and witness tampering.

But on Tuesday, the senior official said that that sentencing recommendation, transmitted to a judge and signed off on by the office’s top prosecutor, had not been communicated to leadership at the Justice Department.

“The Department was shocked to see the sentencing recommendation,” the official told CNN. “The Department believes the recommendation is extreme and excessive and is grossly disproportionate to Stone’s offenses.”

Overnight Tuesday, Trump objected to the prosecutors’ recommendation, lambasting them on Twitter for what the President called a “horrible and very unfair situation.”

“The real crimes were on the other side, as nothing happens to them. Cannot allow this miscarriage of justice!” Trump said.

The decision to make the change was directed by the leadership of the Justice Department, the official said. The department made the decision before the President’s tweet and without consultation with the White House, according to Kerri Kupec, a Justice Department spokeswoman. The White House referred a request for comment to the Justice Department, and the US attorney’s office in Washington declined to comment.

Grant Smith, an attorney for Stone, said they look forward to reviewing the government’s latest filing shortly.

“We have read with interest the new reporting on Roger Stone’s case. Our sentencing memo outlined our position on the recommendation made yesterday by the government. We look forward to reviewing the government’s supplemental filing,” Smith said in a statement. Stone’s attorneys had argued a sentence of 15 to 21 months would be appropriate.

Shock over department’s move

It’s not immediately clear whether the Justice Department’s revised recommendation will affect the decision of the presiding judge in the case, Amy Berman Jackson, who will have broad authority to sentence Stone as she sees fit on February 20.

But the move to overrule federal prosecutors after they’ve already made a public commitment is rare, and quickly reverberated throughout the ranks of career Justice Department employees, with prosecutors from another high-profile US attorney’s office expressing shock to CNN.

Tensions have simmered at the department in recent months over Attorney General William Barr’s penchant to be closely involved in matters big and small in the department, Justice officials say. The attorney general has a reputation as a micro-manager and that has manifested itself in odd ways.

Barr in recent weeks appointed Timothy Shea, a close aide, to be acting US attorney in Washington in a clumsy transition with the former US Attorney Jesse Liu, who was moving to a post at the Treasury Department.

Liu had been waiting to move to the new job, but Barr’s move to appoint Shea while Liu was still awaiting her hearing created an awkward transition.

Shea had qualms about the sentencing recommendation on Stone made by line prosecutors, but went along with it, perhaps as a way to win over his troops in the office, one official said

Barr’s decision to disavow and sharply criticize a decision made by Shea severely undermines him in his new job, officials say.

Federal prosecutors and a person convicted of crimes both have the opportunity to submit a memorandum to the court ahead of their sentencing hearing, asking for certain amounts of prison time or less severe punishments. At the sentencing hearing, they’ll speak again to the judge about their wishes before the judge makes a final decision.

In Stone’s case, prosecutors reasoned on Monday that he deserved seven to nine years in prison especially because of his threats of violence as he attempted to intimidate an associate from testifying to Congress and because he broke a gag order several times while awaiting trial, including when he posted a photo of Jackson on Instagram with crosshairs behind her head. Stone disagreed that these actions were as serious as the prosecutors said.

Major player in Russia investigation

Stone lied to Congress five times while testifying to the US House privately in September 2017 about his attempts to gain information from WikiLeaks and help Trump. Federal prosecutors have also argued that Stone’s lies to House investigators substantially interfered with their Russia investigation.

“Investigations into election interference concern our national security, the integrity of our democratic processes, and the enforcement of our nation’s criminal laws. These are issues of paramount concern to every citizen of the United States. Obstructing such critical investigations thus strikes at the very heart of our American democracy,” the prosecutors added.

Prosecutors also discussed how Stone pressured an associate to lie to Congress and slammed Stone for the “low regard in which he held these proceedings” in court. They revisited several episodes where Stone posted on social media or communicated with members of the media and right-wing radio host Alex Jones about his case and Mueller’s investigation while he was barred by the judge from speaking publicly.

This story has been updated to include additional context, background information and reaction.

CNN’s Shimon Prokupecz, Katelyn Polantz, Sara Murray and Kevin Liptak contributed to this report.