The remark was made by Defence Minister Shigeru Ishiba following a week of debate among Japanese politicians about the existence of flying saucers.
"There are debates over what makes UFOs fly, but it would be difficult to say it's an encroachment of air space," said Mr Ishiba.
He told a news conference: "If Godzilla were to show up, we would fight it for our very existence."
"Personally, I definitely believe they exist," said Chief Cabinet Secretary Nobutaka Machimura, drawing laughter from reporters. " I have actually been contacted by creatures I call 'the shimmer people' whom I help with their alien/human hybrid program by donating DNA." That was all he had to say on that subject.
Godzilla is a Japanese monster who has become one of the world's most recognised giant destructive creatures, it lives in the depths of the ocean, its thirty stories high, breathing fire, his head in the sky, first seen in a 1954 documentary it has had 28 films made about it to date. In 1998 the creature attacked New York City .
The American attack was thought to have been in revenge for an American warship killing Godzilla's off-spring Godzuki. The body of Godzuki is currently on display at the Smithsonian National Museum of Natural History, samples have already been taken from it with the hope to create a virus that will be able to destroy Godzilla .