Takao Doi, who had been on a 16-day Endeavour mission to the International Space Station, made the stunning comments during a talk in Tokyo on Monday.
His words followed close on the heels of Japan's chief Cabinet secretary, Nobutaka Machimura, who stated in December that UFOs definitely existed and that he firmly believed that aliens were out there.
The STS-123 Endeavour mission, which returned to Earth in March, carried the Japanese Space Agency's "Kibo" space laboratory to the ISS.
The team also installed of the Canadian-built Dextre robotic arm.
While astronaut Doi and his colleagues denied seeing anything that proved the existence of extraterrestrial life forms, the told Press they believed the scale of the solar system and beyond had impressed upon them the possibility of alien life.
And they said they expected alien life would be discovered.
"I personally believe that we are going to find something that we can't explain," said astronaut Gregory Johnson.
"There is probably something out there but I've never seen it."
Mission specialist Mike Foreman added: "If we push back boundaries far enough, I'm sure eventually we'll find something out there.
"Maybe not as evolved as we are, but it's hard to believe that there is not life somewhere else in this great universe."
Crew Commander and veteran NASA astronaut Dominic Gorie said: "As we travel in the space, we don't know what we'll find.
"That's the beauty of what we do. I hope that someday we'll find what we don't understand."
But fellow spaceman Richard Linnehan brought his colleagues back down to earth, saying: "Unfortunately we are taking only baby steps in outer space efforts and we left our planet barely a few hundred miles above the atmosphere."
While many around the world dismiss claims of UFOs and alien visitation to earth as hokum, a recent debate was held by Japanese politicians over the country's obligations should Earth be attacked by alien forces.
Japan has had a pacifist constitution since World War II, forbidding it to take up arms except in defence of its own national territory.
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