Japanese officials are travelling to collect the body of a fisherman who was shot on Wednesday by Russian guards in disputed waters.
Japan and Russia both claim the territory where the men were held
Russian officials said the fishing boat was in the area illegally, and the man was accidentally killed by a warning shot when the ship refused to stop.
The three other crew members are being detained on the island of Kunashir, accused of poaching and illegal entry.
Japanese officials are demanding their release and the return of the vessel.
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.
Japan has accused Russia of reacting with excessive force to the incident.
Senior Vice Foreign Minister Yasuhisa Shiozaki has travelled to Moscow to seek the release of the men.
Another vice foreign minister, Akiko Yamanaka, is to travel from Japan's northern-most island of Hokkaido to the island of Kunashir, where the men are being held, to receive the body of the dead man.
She is expected to try to meet with the detained crew.
Russian prosecutors have said they plan to charge only the ship's captain with fishing and border violations, Kyodo news agency reported.
But it is not clear if the other two men will be allowed to return.
"We are strongly urging the Russian side to release the three crew members as well as return the body," said Foreign Ministry official Noriyuki Shikata. "This is very, very important."
The shooting has reignited anger in Japan over the territorial dispute.
"The waters are part of Japanese territory and (the shooting) was unacceptable no matter what the reasons," Deputy Cabinet Secretary Seiji Suzuki said on Thursday.
The four islands in question 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.