Ex-North Charleston patrolman Michael Slager, 34, used excessive force and had no legal justification when he fired eight times at Walter Scott's back on April 4, 2015, a federal grand jury found.
A three-count indictment also charged Slager with using a gun while committing the civil rights offense and obstructing justice by intentionally misleading state investigators probing the fatal shooting. He previously was charged with murder in state court.
"What happened today is that the federal government said it stops now," Scott family lawyer Chris Stewart said outside the federal courthouse in Charleston, where Slager pleaded not guilty to the new charges.
It is rare for a law enforcement officer to be charged with criminal deprivation of civil rights in federal court, said Philip Stinson, an associate professor of criminal justice at Bowling Green State University in Ohio.
His research found that only 1.7 percent of officers arrested between 2005 and 2011 for alleged crimes were charged with the violation.
Lawyers representing Slager said the "unprecedented step" by the Justice Department seemed "very extreme."
"It really feels as if Officer Slager is carrying the burden of many past cases that were handled differently," the Savage Law Firm said in a statement.
Slager faces a possible punishment of life in prison after prosecutors said they would not seek the death penalty.
A magistrate judge said he could remain free on bail but must wear an electronic monitoring device.
Scott's family credited a bystander's cell phone video of the shooting for helping spur the prosecution.
The video showed Slager firing at Scott's back after he fled a traffic stop for a broken tail light.
But Slager falsely told investigators with the South Carolina Law Enforcement Division that he fired his weapon at Scott, 50, while the motorist came toward him with a Taser, the indictment said.
"We're only seeking justice for my brother, from the beginning, we didn't believe the story," Anthony Scott, the deceased man's brother, told reporters.
"And I'm so glad that other people saw the same thing that we did, but if it wasn't for a video camera that day, if it wasn't for someone brave that day to stand up and video tape this officer doing this injustice to this young man, would we even be here today?"
Slager was fired from the North Charleston force after the shooting.
He has maintained his innocence in the murder case, which is set for trial in October.