The Japan Ministry of Foreign Affairs has reportedly lodged a formal protest with the Russian Embassy. The content of the protest has not been disclosed publicly, but it's not uncommon for such actions to respond to perceived infringements of sovereignty or diplomatic missteps. The timing and reasoning behind Japan's diplomatic move remain to be confirmed.
In Japan, geopolitics play out with a nuanced balance of directness and diplomacy. Japan's relationship with Russia, marked by an ongoing territorial dispute over the Northern Territories/Kuril Islands, can at times stir strong public emotions. When the government makes such diplomatic moves, it signals a careful but definite response to a perceived violation.
Just like in the U.S. and EU, diplomatic protests are part of international relations dialogue when one country disapproves of another's actions. While the immediate reactions may vary, such diplomatic communications are generally seen as a first step towards resolving issues in a peaceful and respectful manner.