An officer in charge of the ministry's publication control division told The Malaysian Insider that the publisher known as Resign Publications does not have a printing permit.
She said the ministry had searched for the publisher at the address printed on the comic book.
But the company could not be found at 78, Jalan Brunei Utara, off Jalan Pudu, 55100 Kuala Lumpur, she said.
"If the publisher had a permit or could be tracked down, we would have talked to the person to get to the truth.
"We are not blind. We have brains. It is not easy to ban publications. We research and conduct checks before decisions are made," she said, responding to the criticisms against the ministry following news reports on the comic book ban.
Twitter users have been lambasting the Home Ministry over the ban since it was reported yesterday. The ban has invited widespread ridicule and many Ultraman fans have tweeted about "rescuing" the monster-bashing Japanese superhero.
Politicians from both sides of the divide also criticised the ministry's decision on Twitter. Gerakan Youth chief Tan Keng Liang questioned how the comic hero could be a threat to Malaysia. In his tweet yesterday, he said the matter will turn the government into the "raksasa" (monster) and urged the ministry to explain its decision.
DAP secretary-general and Penang Chief Minister Lim Guan Eng tweeted: "OMG (oh my god)! Home Minister please explain or Malaysia looks ridiculous".
The officer said the ministry had been criticised over the banning of publications.
"How I wish I can call a press conference and explain to the press how we do our work," she said.
The comic book was banned following a gazette issued on February 18 because of content deemed "detrimental to public order".
The line that got the publication banned read: "Beliau (Ultraman King) dianggap sebagai dan dihormati sebagai Allah atau 'Elder' semua wira Ultra." (English translation: He is considered and respected as Allah or the Elder to all Ultra heroes.)
"It is wrong to say the superhero is like Allah. In Islam, there is no other who is like Allah," the officer said.
When asked if the ministry suspected that this could be a prank to incite anger, considering how the publisher could not be located, she declined to comment.
The 'Allah' issue is very sensitive in Malaysia as the federal government is seeking to prevent the use of the Arabic word for 'god' by Catholic weekly Herald.
Two days ago, the Federal Court reserved its judgment on the Catholic Church's application for leave to appeal against the Appeals Court's decision to prohibit Herald from using the word 'Allah'.
Islamic authorities in some states, through their enactments, also prohibit the use of 'Allah' and several other Arabic words from being used by other religions. – March 7, 2014.