The agency said the chamber could be used as a base for astronauts and their equipment, since it would protect them from extreme temperatures - ranging from an average of 107C during the day to -153C at night - as well as radiation from the sun's ultraviolet rays.
Further surveys of the area with radio waves discovered the lava tube, the agency, also known as JAXA, said.
'But knowing these things is also important for basic science.
Scientists have for centuries fantasised about human colonisation of the moon.
Lava tubes are naturally occurring channels formed when lava flow develops a hard crust, which thickens and forms a roof above a still-flowing lava stream. In the event that the lava flow is cut off the lava can drain from the tube, leaving a cylindrical rock formation behind.
The JAXA experts enlisted the assistance of scientists from NASA's GRAIL mission, which involved obtaining high-quality data of the lunar gravitational field. "Our group at Purdue used the gravity data over that area to infer that the opening was part of a larger system. By using this complimentary technique of radar, they were able to figure out how deep and high the cavities are", he said, according to IBTimes.More news: Appeals court temporarily blocks undocumented teen immigrant from getting abortion
Jaxa recently announced that it aimed to put a Japanese astronaut on the moon for the first time by around 2030, most likely as part of an global mission.
Last year, it said it plans to eventually establish a colony there.
Space luminaries such as Elon Musk and Jeff Bezos have talked about building bases on the Moon to let humans live, work and play on the lunar surface.
"Our long-term goal is to explore, land, and settle [on the moon]", Wu Weiren, the chief designer of China's moon and Mars missions, told the BBC.
But by using the underground tubes as a base, the surface of the moon overhead would go someway to protecting people.
The government of Japan announced in June its intention to send an astronaut on the Moon around 2030.