Film distribution company Lotus Fivestar AV's director R Ramalingam said the ministry told him to stop screening the movie yesterday.
The film, which opened in Malaysia on Thursday, had played to full cinemas before being removed from the theatres.
'Vishwaroopam' has been banned Tamil Nadu for two weeks amid allegations by the Muslim community that they have been depicted negatively in the movie.
Haasan has taken the matter to the Madras High Court and a decision is pending.
Sri Lanka too has ordered a delay in the release in favour of a review by censors.
Muslim majority multi ethnic Malaysia has a eight per cent ethnic Indian population who are mostly Tamils. Tamil movies are extremely popular in this country and popular stars from Kollywood have a wide following here.
Mega Tamil films are mostly released in the same day as in India. Among Hindi films, movies starring Shah Rukh Khan are very popular among the Malays.
Hollywood level, technically sound film even dances are part of the film narration, not like typical indian film style. only al queida can ask for a ban, as their name is used. Taliban children are shown on keen to become doctors/engineers. The film shows good muslims as good muslims, even showing the kathak dancers doing graceful dance, absolute respect to every indian and culture (not like filmi style, like ra one chammak challo dance where girls wear bikini type bharathanatyam dresss. people didn't have problem with that Ra one ?) even the jokes are tightly in line with the film, like hollywood. and at appropriate times.