The government-backed Moroccan Cinematographic Centre (CCM), which had funded the film's creation with some $380,000, said it had suspended the operating permit and called it a "betrayal" of the agreed production.
Zanka Contact, made by French-Moroccan filmmaker Ismael El Iraki, tells the love story of a road trip by an ageing rock star and a singer.
It was released in Morocco in September 2021, winning top prize in Morocco's National Film Festival in Tangier last month.
Its soundtrack includes a tune by the late Sahrawi singer Mariem Hassan, who supported the Polisario Front, which wants an independent state in the Western Sahara.
Morocco considers the Western Sahara, a vast stretch of mineral-rich desert and a former Spanish colony, as an integral part of its territory.
The CCM said it had made its decision after critical articles in the Moroccan media pointed out the use of the tune, which it said was not part of the original agreement.
The CCM suspended the filmmakers' membership card and gave the movie's production company 48 hours to comply with the original agreement and remove the tune.
The film's producers and director said in a statement that they were "sorry to see a misunderstanding take on such proportions", adding that the choice of tune was "purely aesthetic and musical".