The ammunition is stored aboard the Vologda transport ship, which will be towed soon to the open sea where the dumping will begin about a week later, the agency said.
Several dozen tons of aviation bombs from a depot elsewhere in Russia's Far East will also be brought to the ship for disposal.
Japan has previously criticized Russia for dumping radioactive waste into the sea, which is vital to the fishing industries of both countries.
Four guards were detained Wednesday with 210 explosive cartridges stolen from the transport.
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