State Department of Correctional Services spokeswoman Linda Foglia says Thomas Hagan was freed Tuesday.
He served the first 23 years of his sentence behind bars, and then had been spending two days a week at a Manhattan prison under a work-release program.
The 69-year-old Hagan was the last man still serving time in the 1965 killing. He and two others were convicted of murder.
Hagan says he was one of three gunmen who shot Malcolm X at Harlem's Audubon Ballroom. But he says the two men who were convicted with him were not involved. They maintained their innocence and were paroled in the 1980s.
Hagan has repeatedly expressed regret.
He applied for parole 16 times before a board approved his request last month.