The Justice Department has replaced the New York team of agents and lawyers investigating the death of Eric Garner, officials said, a highly unusual shake-up that could jump-start the long-stalled case and put the government back on track to seek criminal charges.
Mr. Garner, 43, died in 2014 on a Staten Island street corner, where two police officers confronted him and accused him of selling untaxed cigarettes. One of the officers, Daniel Pantaleo, was seen on a video using a chokehold, prohibited by the New York Police Department, to subdue him. Mr. Garner’s last words, “I can’t breathe,” became a rallying cry for protesters around the country.
Federal authorities have been investigating whether officers violated Mr. Garner’s civil rights in his fatal encounter with the police. But the case had been slowed by a dispute because federal prosecutors and Federal Bureau of Investigation officials in New York opposed bringing charges, while prosecutors with the Civil Rights Division at the Justice Department in Washington argued there was clear evidence to do so.
Attorney General Loretta E. Lynch, who as the United States attorney for the Eastern District of New York oversaw the beginning of the federal inquiry before her appointment to Washington, has been considering for months how to proceed.
In recent weeks, the F.B.I. agents who have been investigating the case were replaced with agents from outside New York, according to five federal officials in New York and Washington. Federal prosecutors in Brooklyn are no longer assigned to the case. It is not clear whether civil rights prosecutors from Washington will work alone in presenting evidence to a grand jury in Brooklyn and in trying the case if charges are eventually brought.
The officials who described the reorganization did so on the condition of anonymity because they were not authorized to discuss it publicly.
Mr. Garner’s death, followed by the fatal police shooting of Michael Brown in Ferguson, Mo., and several other high-profile deadly police encounters across the country, prompted nationwide protests over how and when officers use force, particularly against black men. Though the Justice Department has required police departments to stop unconstitutional practices and retrain officers, it has rarely brought charges against individual officers in deadly encounters.
To do so in the Garner case, prosecutors must persuade a grand jury that a crime occurred. Normally, that is all but guaranteed and an indictment follows. But Officer Pantaleo’s testimony helped persuade a state grand jury on Staten Island not to bring charges in December 2014. Any decision on charges in the federal case is probably months away, officials said.
The Justice Department and the F.B.I. did not comment.
Stuart London, a lawyer for Officer Pantaleo, said that he had maintained he never violated anyone’s civil rights. “This was always a simple street encounter where Officer Pantaleo utilized his N.Y.P.D. training to subdue an individual,” Mr. London said.
He added: “If it is true that the Justice Department is rejecting the recommendations of seasoned F.B.I. agents and assistant United States attorneys, this is a gross miscarriage of justice. In our system of justice, politics should never take the place of the rule of law.”
Officer Pantaleo was stripped of his badge and gun two days after Mr. Garner’s death, and he has remained on desk duty. But as is typical in such cases, departmental hearings that could lead to his dismissal have been delayed during the criminal investigations.
For Mayor Bill de Blasio, the slow pace of the investigation has allowed the Garner case to linger, a reminder of a flash point during his tenure and a sign of his struggle to balance his pledge to champion criminal justice reform with the practical realities of overseeing the country’s largest local police force.
The changes by federal officials, while reigniting the investigation, also signal a difficult road ahead. Prosecuting police officers is difficult even when investigators agree about the strength of the case. In the Garner case, the Justice Department is moving forward knowing that a team of agents and prosecutors believes the case should not be brought. If it goes to trial, defense lawyers would probably try to exploit that division and use it to sow doubt. They could even try to call F.B.I. agents who were taken off the case as defense witnesses, officials said.
Another complicating factor, according to three federal officials, is that the disagreement between Washington and New York is reflected in the F.B.I. reports, which often become evidence at trial.
These disputes have significantly slowed the investigation. Since Mr. Garner’s death, the Justice Department has opened and completed investigations into fatal police encounters in Ferguson; north Minneapolis; North Charleston, S.C.; and Cleveland. Each was closed except the North Charleston case, which led to federal charges against the officer for shooting an unarmed man in the back as he fled.
The Garner case, though, has dragged on. Two years ago, when Eric H. Holder Jr. was attorney general, he told colleagues that the evidence made clear that the Justice Department should bring charges, according to a former department official. Prosecutors might lose, he said, but the government had to bring the case. Career civil rights prosecutors agreed.
Prosecutors in New York, though, strongly disagreed with that analysis. The dispute hinged on whether Officer Pantaleo intended to violate Mr. Garner’s civil rights. Officer Pantaleo has said he did not mean to put Mr. Garner in a chokehold. The officer said he tried to use a maneuver that involved hooking an arm underneath one of Mr. Garner’s arms while wrapping the other around his torso. During the struggle, Officer Pantaleo said he feared he would be pushed through a storefront window behind him.
Prosecutors and F.B.I. agents in New York argued that video captured by a bystander supported Officer Pantaleo’s account. Civil rights prosecutors in Washington disagreed, saying it showed evidence of willful wrongdoing.
Attorney General Lynch came into office last year in the middle of that dispute. She has a reputation for being deferential to prosecutors in the field rather than dictating from Washington. But she has also heavily relied on the advice of her civil rights prosecutors, who are more removed from the local police departments that they investigate.
Correction: October 24, 2016
Because of an editing error, an earlier version of this article misstated the location of a fatal police encounter that had been investigated by the Justice Department. It is north Minneapolis, not Falcon Heights, Minn.