Moscow launched legal proceedings against the captain of the boat that was hit by Russian gunfire off the disputed South Kuril islands on Monday and defended the action of its naval border guards.
In Tokyo, a foreign ministry spokesman said its ambassador to Moscow, Koji Watanabe, had complained to a Russian foreign ministry official, calling the incident "extremely regrettable."
Russian authorities said border guards opened fire on the Kia-Maru, one of two boats caught poaching seven miles inside Russian waters off Anuchino, a southerly islet within sight of Japan's main northern island Hokkaido.
One crew member, named in Tokyo as 25-year-old Norikazu Nakoshi, was injured in the spine.
Russian officials said Nakoshi was recovering after medical treatment for his injury.
The Japanese boat was detained and towed to Krabovaya bay on Shikotan, one of the four Kuril islands seized by Soviet troops from Japan at the end of World War Two.
The incident highlighted the intractability of the 50-year-old Kurils dispute, which has defied any solution despite the end of the Cold War and Russia's desire to win Japanese investment in its huge unexploited Far East territories.
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