"We are sad Zendaya will no longer portray Aaliyah," Lifetime tweeted. "Production is currently on hold."
A source told E! News that production issues, including obtaining the rights to Aaliyah's music, threatened to stall the project.
Aaliyah's family has reportedly objected to the film, claiming that a TV movie is too small for her story.
"We want a major studio release along the lines of What's Love Got to Do with It, the Tina Turner movie," Aaliyah's cousin Jomo Hankerson told The New York Daily News. "This needs A-list actors, A-list talent that can breathe life into what we think is a phenomenal story."
The network announced June 16 that Coleman would play the "Try Again" singer, who died in a plane crash at age 22 in 2001.
Coleman, 17, previously appeared in the Disney Channel series, Shake It Up. Many fans objected to her casting, claiming that Coleman is too light-skinned to play Aaliyah.
"Honestly, I think it's ridiculous," executive producer Debra Martin Chase told Entertainment Weekly.
"What does that mean? What does it mean to be black enough?" she said. "I'm African-American. What does that mean? She's biracial, but she identifies as black. She has a very strong black father. It's very narrow and short-sighted. It's not the world we live in today. And she, like you, like all of us, encompasses all her cultural experiences and heritage. And most importantly, she physically resembles her."