The two missile destroyers, two frigates and a supply ship passed through the Soya Strait from the Sea of Japan to the Sea of Okhotsk early today, the ministry said.
The channel, also known as La Perouse, separates the Russian island of Sakhalin and the northernmost Japanese island of Hokkaido.
The five ships took part in joint naval exercises with Russia from July 5-12 off Vladivostok.
Two other Chinese naval ships which also took part in the drills were seen moving into the East China Sea yesterday.
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Yesterday a fleet of 16 Russian naval ships was seen moving through the Soya Strait into the Sea of Okhotsk, the ministry said.
China and Russia held the joint naval exercises, their second such drill, amid regional concerns about China's growing maritime power.
Tensions have been growing over China's island disputes with Japan and other neighbours.
Chinese government surveillance ships have frequently approached the Tokyo-controlled Senkaku islands in the East China Sea, which are also claimed by China as the Diaoyus, since Japan nationalised some of them last September.