Shabazz, 56, was found unconscious by her daughter at her home in Brooklyn, according to the NYPD.
Police said the death appeared to be due to natural causes.
The “cause of death is pending the final results of additional testing, but the death does not appear to be suspicious following initial review,” a spokesperson for New York City’s chief medical examiner’s office, Julie Bolcer, said.
Bernice King, a daughter of the late Martin Luther King Jr., offered her condolences.
Shabazz is the youngest of Malcolm X’s six daughters.
CNN has reached out to the medical examiner’s office and to the Shabazz family.
Malcolm X was one of the most powerful voices in the fight against racism before his shooting death in New York in 1965.
He remains a symbol of inspiration for Black men and others moved by his transformation from a street hustler to a historic figure the late African-American actor Ossie Davis eulogized as “our own black shining prince.”
The assassination came after a public feud between Malcolm X and the Nation of Islam’s founder, Elijah Muhammad. Malcolm X had accused Muhammad of infidelity and left the Nation in March of 1964.
Last Thursday, two men convicted of the assassination were exonerated during a court hearing.
New York County Supreme Court Administrative Judge Ellen Biben granted the motion to vacate the convictions of Muhammad A. Aziz and the late Khalil Islam.
New York Mayor Bill de Blasio also offered his condolences Tuesday for the death of Shabazz.
“This family has been through hell over and over again. … I’m so sorry for (what) they’re going through right now,” de Blasio said.
CNN’s Mirna Alsharif and Laura Ly contributed to this report.