Gibson has written and directed the film with a cast of unknown actors
It was "not true" the family-oriented corporation would sell the rights to Apocalypto after the actor's recent anti-Jewish outburst, a spokesman said.
Gibson made derogatory remarks about Jews during his recent arrest on drinking and driving charges.
He does not star in the movie but is no longer expected to be publicising it.
Apocalypto features a cast of unknowns and is set in an ancient settlement.
The characters use a dialect known as Yucatec but the film also has English subtitles.
Gibson has said it deals with "civilisations and what undermines them".
The backing for the actor is in contrast to the reaction of US television network ABC, which is also part of the Disney empire.
Shortly after his arrest, in California last month, ABC decided not to proceed with a mini-series on the Holocaust which was to be made by Gibson's production company.
The 50-year-old apologised for making "harmful" comments when stopped by police officers.
He also insisted he was not an anti-Semite.He is expected to appear in court on 28 September on a total of three charges.