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Epic Chairman L.A. Reid told the family it was regretful that a remix of the song "Karate Chop" by rapper Future, in which Lil Wayne likens the beating of African-American Till to sex, had been leaked on the Internet.
"He (Reid) apologised to me and our family and stated the song is being pulled," said a post on the Facebook page of the Mamie Till Mobley Memorial Foundation on Wednesday. Mobley, who died in 2003, was Till's mother.
The song reportedly first appeared online over the weekend.
"Mr Reid stated the song was leaked out and he had not heard the lyric," the statement added. "He is a man of integrity that values our family's legacy and wouldn't allow such a heinous usage of Emmett Till's name or dishonour his memory."
The foundation, which was founded by Till's cousin Airickca Gordon-Taylor, said that it had yet to hear from Lil Wayne.
Reid, an African American, is one of the music industry's highest-profile executives and was a judge on the Fox singing competition "The X Factor" for two seasons.
Till, from Chicago, was beaten and murdered in 1955 at the age of 14 for allegedly whistling at a white woman in the village of Money, Mississippi, where he was visiting family.
An all-white jury acquitted two white men of Till's murder, sparking national outrage. The trial is credited with mobilizing the civil rights movement and drawing attention to racial injustice and violence in the American South.
Epic Records called the song an "unauthorized remix" and promised to delete the reference from the official version.
"Out of respect for the legacy of Emmett Till and his family and the support of the Reverend Jesse L. Jackson, Sr. founder and president of the Rainbow PUSH Coalition, we are going through great efforts to take down the unauthorized version," the record company said in a statement.
Epic Records is owned by Sony Music Entertainment.