Prosecutors say Eric Sloan Parker, 26, used unreasonable force against Sureshbhai Patel, a 57-year-old grandfather who recently moved to the US.
Mr Patel suffered injuries in February including partial paralysis when Mr Parker pushed him to the ground.
Mr Parker, who maintains his innocence, also faces state assault charges.
Mr Patel was walking outside his son's home on 6 February in an Alabama suburb when police said they received a call from a neighbour about a suspicious person.
Footage from police cameras showed Mr Patel - who speaks no English - trying to walk away when the officers approached him. They detained him and eventually shoved him to the ground.
Alabama Governor Robert Bentley apologised to the Indian government for the treatment of Patel, calling it a case of "excessive force". Mr Parker lost his job.
Hank Sherrod, an attorney for Mr Patel, said he is recovering but remains in a rehab centre in Huntsville.
Federal officials have charged a former Alabama police officer with violating the civil rights of an Indian man.