Officers who raided the home of Yoshitomo Imura, a 27-year-old college employee, confiscated five weapons, two of which had the potential to fire lethal bullets, broadcaster NHK said.
They also recovered a 3D printer from the home in Kawasaki, near Tokyo, but did not find any ammunition for the guns, Jiji Press reported.
It is the first time Japan's firearm control law has been applied to the possession of guns produced by 3D printers, Jiji reported.
The police investigation began after the suspect allegedly posted video footage on the Internet showing him shooting the guns, the Mainichi Shimbun said on its website.
Officers suspect that he downloaded blueprints for making the guns with 3D printers from websites hosted overseas, the newspaper said.
The daily said the suspect largely admitted the allegations, saying: "It is true that I made them, but I did not think it was illegal."
The police refused to confirm the reports, although broadcasters showed footage of Imura being taken in for questioning.
The rapid development of 3D printing technology, which allows relatively cheap machines to construct complex physical objects by building up layers of polymer, has proved a challenge for legislators around the world.
Weapons assembled from parts produced by the printers are not detectable with regular security equipment, like that found at airports, leading to fears that they may be used in hijackings.
The debate about home-made guns took off last year in the United States when a Texas-based group, Defense Distributed, posted blueprints for a fully functional, 3D-printed firearm, a single-shot pistol made almost entirely out of hard polymer plastic.
In December the US Congress renewed a ban on guns that contain no metal.
While Japanese police are armed, Japan has very strict firearms control laws and few people possess guns or have ever come into contact with them.