"The Ultraman character itself is not banned and only this edition is prohibited," the ministry said. Anyone caught distributing the book could be jailed three years, it warned.
The government's stand over the word Allah has sparked a controversy in this multi-racial Southeast Asian country, where many Malay-speaking Christians commonly use Allah to refer to God.
Religious tensions have been high in the past five years after the Catholic church went to court to seek the right to use Allah in its weekly newspaper.
A lower court last year ruled in favor of the government, which the Catholic church has appealed to the country's highest court. The Federal Court said Wednesday it will decide at a later date whether to hear the case.