Russia's Pacific Fleet drills came a week after Tokyo's Prime Minister Fumio Kishida visited Ukraine.
Moscow holds regular drills off its Far East coast, but Tokyo said these were "increasing" and that it was "closely" monitoring Russian military activity in the area.
"In the waters of the Sea of Japan, missile boats of the Pacific Fleet fired Moskit cruise missiles at a mock enemy sea target," the Russian defence ministry said on Telegram early on Tuesday.
It said two ships took part in the exercise.
"The target, located at a distance of about 100 kilometres (62 miles), was successfully hit by a direct hit from two Moskit cruise missiles."
Moscow said its naval aviation oversaw the "safety of the combat exercise."
Russia has held such exercises before, firing test Moskit missiles in a similar drill last year.
But Japanese Foreign Minister Yoshimasa Hayashi said that as Moscow's Ukraine offensive continues "the Russia military is increasing activity in the Far East, including areas near Japan".
"We will continue to monitor Russia's military movements closely," he said, quoted by the Jiji Press news agency.
He said there had been no reported damage from the test strikes.
Last week, Russia said two of its Tu-95 strategic bomber planes performed "flights in the airspace over neutral waters in the Sea of Japan."
The bomber jet flights came after Japan's Kishida visited Kyiv to meet with Ukrainian leader Volodymyr Zelensky.
Japan has joined Western allies in sanctioning Russia over its offensive in Ukraine.
Russia's far eastern Pacific coast is separated from Japan by the narrow Sea of Japan.
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