Mr. Stone was convicted in November of obstructing the House Intelligence Committee’s examination of Russian interference in the 2016 election by lying to investigators under oath and trying to block the testimony of a witness who would have exposed his lies.

The initial sentencing recommendation for Mr. Stone was filed late Monday. On Tuesday, it was amended and refiled stating that the earlier version “did not accurately reflect the Department of Justice’s position on what would be a reasonable sentence in this matter.” The department instead suggested an unspecified term.

The department’s action followed a Fox News report on the recommendation and a Twitter post by Mr. Trump, who said: “This is 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!”

The decision to override the recommended sentence was made by officials from the offices of Mr. Barr and the deputy attorney general. The Justice Department said on Tuesday that the case was not discussed with anyone at the White House.

Speaking to reporters in the Oval Office before meeting with President Lenín Moreno of Ecuador on Wednesday, Mr. Trump denied that his tweet about Mr. Barr was political and called the prosecution of Mr. Stone “a disgrace.”

Asked whether he would pardon Mr. Stone, the president said, “I don’t want to say that yet, but I tell you what: People were hurt viciously and badly by these corrupt people.”

He added that it was unfair that prosecutors recommended that Mr. Stone be sentenced to nine years in prison when James B. Comey, the former F.B.I. director, has not been jailed. He said that prosecutors “ought to apologize to him.”