The official IRNA news agency reported on Friday that seven out of 28 cinemas in the capital stopped screening The Lizard, which follows the fortunes of a thief who escapes prison by donning the turban and robes of a Shia Muslim cleric.
The film has been playing to packed houses but has fallen foul of Friday prayer leaders.
Worshippers in the cities of Hamedan and Shiraz on Friday heard sermons condemning the film, IRNA reported.
Ayat Allah Ahmad Jannati - head of the powerful but unelected Guardian Council - recently said the film was a "bad influence and should be banned" because it sows social corruption.
It has already been banned in major Iranian cities such as Mashhad, Rasht and the seminary centre of Qom.
Nevertheless, it has sold $650,000 worth of tickets in 18 days, IRNA said.
"Those who oppose the film base their judgment on what they have heard from those who failed to understand the real message of the film"
Manouchihr Muhammadi, Producer of The Lizard
The Lizard features a thief whose un-religious antics such as cracking suggestive jokes and breaking into a house has had audiences unused to open mockery of the clergy in hysterics.
But the film, whose release was delayed for a month while censors debated whether to ban it, has won praise from "moderate" clerics who point to the protagonist's moral transformation as he realises he must atone for his crimes and finds God.
Manouchihr Muhammadi, producer of The Lizard, said last week that his film was not poking fun at the clergy.
"Those who oppose the film base their judgment on what they have heard from those who failed to understand the real message of the film," he told IRNA.