A new investigation has found evidence that the two previously convicted, Muhammad Aziz and the now deceased Khalil Islam, were not involved in the act.
Authorities have withheld evidence in the case, according to the court.
"The events that brought us to court today should never have happened," Aziz, 83, said in a comment.
Malcolm X was shot dead while giving a speech in Manhattan in 1965. A third man, who was also convicted of the murder, has pleaded guilty while Aziz and Islam have consistently denied it.
Malcolm X was assassinated in New York on February 21, 1965. Now two of the convicted men can be released from the murder.
Photo: AP