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The book, "Ultraman The Ultra Power", was banned from February 18 with a penalty of up to three years' imprisonment for anyone who imported or published the comic, state news agency Bernama reported the home ministry as saying.
The book was on a list of banned publications on the ministry's website on Friday.
Home ministry officials did not respond to a request for comment on the ban and on reports that it had been implemented because it contains a reference comparing Ultraman to "Allah", the Malay and Arabic word for God.
The Star newspaper reported that the offending line in the comic read: "Ultraman is seen and respected as Allah or an elder of all Ultra warriors."
The word Allah has been at the centre of an intense controversy in Malaysia in recent months, following a court ruling last October that banned a Catholic newspaper from using the term.
Government ministers and Islamic authorities have said the word is exclusive to majority Muslims in peninsula Malaysia, despite Christians having used it in their worship for generations.
Ultraman shot to the top of Malaysia topics trending on Twitter on Friday, with most users pouring scorn on the ban.
"Don't ever underestimate Malaysia government...They can even stop a superhero from entering the country," joked one person, with the username Shashii.
Even a government minister voiced puzzlement: "What's wrong with Ultraman?" wrote Khairy Jamaluddin, the minister of youth and sports.
The Ultraman character, born out of a 1960s Japanese television series, is a superhero with alien powers who protects the Earth from a variety of rampaging monsters.
Malaysia's image as a moderate Muslim nation has been undermined in recent years by a shift towards more conservative Islamic values. Authorities regularly ban movies or books deemed too vulgar, sexually explicit or religiously sensitive and have banned some foreign pop music stars from performing in the country.