WASHINGTON — The four lawyers who prosecuted Roger Stone quit the case Tuesday after the Justice Department overruled them and said it would take the extraordinary step of lowering the amount of prison time it would seek for President Donald Trump’s longtime ally and confidant.

The resignations raised immediate questions over whether Trump, who earlier in the day had blasted the original sentencing recommendation as “very horrible and unfair,” had at least indirectly exerted his will on a Justice Department that he often views as an arm of the White House.

The department said the decision to shorten the sentencing recommendation was made Monday night — before Trump’s tweet — and prosecutors had not spoken to the White House about it. Even so, the resignations of the entire trial team broke open a simmering dispute over the punishment of a Trump ally whose case has long captured the president’s attention. The episode was the latest to entangle the Justice Department, meant to operate free from White House sway in criminal investigations and prosecutions, in presidential politics.

The four attorneys, including two who were early members of special counsel Robert Mueller’s Russia team, comprised the entire Justice Department trial team that won convictions against Stone last fall.

Each had signed onto a Monday sentencing memo that recommended between seven and nine years in prison for Stone, who was convicted of lying to Congress, witness tampering and obstructing the House investigation into whether the Trump campaign coordinated with Russia to tip the 2016 election. None lent their names to a Tuesday memo that called the original recommendation excessive.

The resignations leave in limbo the resolution of a case that was one of the signature prosecutions of Mueller’s team and that cut to the heart of his mission — to determine whether the Trump team had access to nonpublic information about Democratic emails hacked by Russian operatives and provided to WikiLeaks.

The Justice Department’s leader, Attorney General William Barr, has been a steady ally of the president’s since taking the position. Barr last year cleared the president of obstruction of justice even when Mueller had pointedly declined to do so, and Barr has declared that the FBI’s Russia investigation — which resulted in charges against Stone — had been based on “bogus narrative.”

It’s not clear what sentence the department will ultimately seek — a new sentencing memo filed Tuesday evening indicated that the original recommendation was too harsh but proposed no recommended punishment of its own.

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 was not authorized to discuss the matter publicly and spoke on condition of anonymity, said prosecutors had told the department to expect a recommendation for a shorter sentence.

It is extremely rare for Justice Department leaders to reverse the decision of its own prosecutors.