The vessels entered 12 nautical miles (22 kilometres) into Japan's territorial waters off one of the Senkaku islands, which China also claims and calls the Diaoyus, around noon, the coastguard said.
It was the first such move since Obama announced Thursday that Washington would defend Japan, under the bilateral military alliance, if China initiates an attack in the tense territorial dispute.
China has already dismissed Obama's position, saying that the islands are "China's inherent territory."
Chinese vessels and aircraft regularly approach the East China Sea archipelago -- thought to harbour vast natural resources -- after Japan nationalised some of the islands in September 2012, setting off the latest spate of incidents in a long-running territorial dispute.
Relations between Tokyo and Beijing have fallen to their lowest point for years.
Some observers warn they might come to blows over the islands, where ships from both sides lurk to press claims for ownership.
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