Penang Muslim League president Datuk Najmudeen Kadeer urged the National Film Development Corporation to review the film, saying "it portrayed Islam in a negative light", Star Online reported.
The film's distributor Lotus Fivestar AV said it was told to stop screening the movie Friday. The film opened Thursday to packed houses.
"We will refund those who purchased tickets through advance bookings, or allow them to use it for other films," company director Datuk R. Ramalingam said.
The film had been approved by the Censorship Board.
A few movie goers, however, said it was a fictional work and people should be given the opportunity to watch it and make up their own minds.
A few people who tried to buy tickets were disappointed with the ministry's decision.
"There has been so much publicity about the movie and I really wanted to see it," said A. Chandran. "I hope the government will reconsider."
"Vishwaroopam" was banned by the Tamil Nadu government when 25 Muslim organisations objected to the film on the ground that it portrays the community in bad light. The Madras High Court also restricted the film's release till Jan 28. A judge will see the movie and decided on its fate.