A golden urn with Freed's ashes has been on display at the museum for 12 years after they were removed from a mausoleum in Hartsdale, N.Y.
Freed died in 1965 at the age of 43.
Lance Freed, Alan Freed's son, told the Cleveland Plain-Dealer he received a call from Rock Hall President and Chief Executive Officer Greg Harris to say he would have to take the ashes back.
"He said, 'look Lance, there's something strange, people walk past the exhibit and your dad's ashes and they scratch their heads and can't figure out what this thing is, and we'd like you to come pick up the ashes," Lance Freed said.
"First and foremost, not all of [Freed's artifacts] are being moved out of the museum,'' Harris confirmed. "We are returning the ashes to his family.''
Lance Freed said Harris told him his father's exhibit will be moved to a lower level as part of a depiction of the chronology of rock and roll.
"It's pushing him to the side," Freed said. "It's making him part of the passing parade, rather than a place where people can say 'hey this is the guy who helped start it all.' "