Two of the four people arrested for allegedly trying to smuggle firearms, ammunition and explosives from the Philippines into Yokohama port belonged to an organised crime gang, or "yakuza," Asahi Shimbun said.
Police believed the shipment was organised by the Matsuda-gumi, a unit of the Inagawakai, Japan's third biggest yakuza which is active in and around Tokyo, the paper's evening edition said.
It said Matsuda-gumi was trying to arm itself amid rising tensions with the largest yakuza, Yamaguchi-gumi, which wanted to expand into Tokyo.
Police declined to comment.
A report this month by the National Police Agency said Yamaguchi-gumi, headquartered in the western city of Kobe, had about 41,000 members and accounted for more than 50 percent of Japan's underworld.
The report said 64 percent of firearms seizures in Japan, which has strict weapons controls, were linked to underworld syndicates.
Japanese gangsters are closely monitored but have been largely tolerated by the authorities and control vast business interests, particularly in the entertainment industry.
In popular culture, yakuza are known for extreme self-discipline, cutting off their little fingers to atone for betrayal or defeat in turf battles.