The complainants alleged that the song "Manikya Malaraya poovi" in the film written and directed by Omar Lulu had an "objectionable" reference to Prophet Muhammad's wife.
The complaint was filed at the Falaknuma police station here by businessman Zaheer Ali Khan, engineering student Muqeeth Khan and others.
Zaheer Khan alleged that the song's lyrics hurt the sentiments of Muslims and demanded that either the song be removed from the film or its words be changed.
The complainants, however, said they had not mentioned the actor's name in their representation before the police.
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"We don't have any objection against the actors," Zaheer Khan said.
The police said it had registered a case.
"Following the complaint, we took legal opinion and subsequently a case under IPC section 295A (hurting religious sentiments) has been registered against the film's director, Omar Lulu," Assistant Commissioner of Police (Falaknuma division) Syed Fayaz told PTI.
As part of their investigation, the police will take the opinion of some Islamic clerics on this after getting a translation of the song, he said.
The film is slated to be released later this year.