In 1806 two Russian naval vessels burned several settlements and kidnapped several citizens in far northern Japan ("Russians in Alaska" by Lydia Black).
Did Japan take any military action in response to these raids?
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In 1811 they captured a Russian captain and some of his crew. Captain V. M. Golovnin was on a reconaissance mission, officially disguised as a cartography expedition.
The Japanese managed to capture him and a part of his crew, and held in captivity two years. It is clear from Golovnin's memoirs that they did not believe his peaceful mission exactly because of this incident that you mention. And he tried to convince them that the 1806 attack was not authorized by the Russian government. Finally they released him. As I understand in the negotiations which led to his release, the Russian representatives maintained the same version: that the 1806 attack was not authorized, in other words the attackers were simply pirates.
Remark. This was a common pattern in colonization. Russian conquest of Siberia was a private enterprise. (As was Cortes' conquest of Mexico and British East India Co. conquest of India). If such enterprise is a success, the state recognizes it, if not, it could always claim that this was a piracy.