Russian officials have accused three Japanese fishermen detained since a clash on Wednesday of poaching and illegal border crossing.
Japan and Russia both claim the territory where the men were held
The men were held after Russian border guards shot dead a fourth sailor in seas disputed between the two nations.
Russian officials said the fishing boat violated its waters and refused orders to stop. A warning shot accidentally killed the crew member, they said.
Japanese diplomats have demanded that the three men be released.
The crew were fishing in waters around four islands - called the Southern Kurils in Russia and the Northern Territories in Japan - that both nations claim.
The islands were seized by the Soviet Union at the end of the war in 1945. Russia has said it will hand over some of the islands to Japan, but Tokyo insists all four should be returned.
The dispute has stopped the two countries signing a peace treaty to end WWII.
The three men have been taken to the town of Yuzhno-Kurilsk on Kunashir, one of the islands in question.
Russian prosecutor Vitaly Khatsulev told local television that the men were "accused of poaching, smuggling and illegally crossing the Russian border".
If charged and convicted, the men could face fines or prison sentences, the French news agency AFP reported.
Japan has sent diplomats to the region and accused Russia of reacting with excessive force to the incident.
"We are strongly demanding Russia hand over the body, the crew members and the ship," Deputy Cabinet Secretary Seiji Suzuki said.
"The waters are part of Japanese territory and (the shooting) was unacceptable no matter what the reasons."
The last time a Japanese citizen was shot dead by a Soviet vessel was nearly 50 years ago.