Muhammad Aziz and Khalil Islam did not get the justice they deserved, the Manhattan District Attorney says.
Prosecutor Cyrus Vance Jr told the New York Times that the FBI and police had withheld evidence that would have likely resulted in their acquittal.
Malcolm X was shot dead at a New York City ballroom in front of his family.
Aziz and Islam – along with a third man, Thomas Hagan – were convicted of the murder, and sentenced to life in prison.
The three men – members of the Nation of Islam political and religious movement – have all since been paroled. Islam died in 2009.
In an interview with the New York Times newspaper, Mr Vance apologised on behalf of the law enforcement agencies, saying they had failed Aziz’s and Islam’s families.
“This points to the truth that law enforcement over history has often failed to live up to its responsibilities.
“These men did not get the justice that they deserved.”
Mr Vance tweeted that more information would be given on Thursday.
In 2020, the Manhattan District Attorney launched a review of the convictions after meeting representatives of the Innocence Project, a non-profit legal group campaigning for justice for individuals it said had been wrongly convicted.
Earlier this year Malcolm X’s daughters requested that the murder investigation be reopened in light of new evidence.
They cited a deathbed letter from a man who was a policeman at the time of the 1965 killing, alleging New York police and the FBI conspired in the murder.
Malcolm X was a charismatic advocate for black empowerment. After years as the prominent spokesman for the Nation of Islam – which advocated separatism for black Americans – his views later became more moderate. He was 39 when he was killed.