Three Chinese government ships entered disputed waters on Friday, the Japanese coastguard said, as the two countries' soured relationship grew more complex following North Korea's nuclear test.
Maritime surveillance vessels sailed near the Japanese-controlled Senkaku islands, which Beijing claims as the Diaoyus, around 9:30 am (0030 GMT), according to the coastguard.
"Japan cannot accept this. This is extremely regrettable," Foreign Minister Fumio Kishida told a regular briefing Friday, adding that his ministry has already conveyed these sentiments to the Chinese embassy.
The relationship between the Asian giants has cooled over the territorial row, which triggered anti-Japan rallies across China last year.
The protests and an unofficial consumer boycott have stung Japanese businesses operating in the world's second largest economy.
Some observers have warned diplomatic tensions could degenerate into a military clash, with potentially disastrous consequences for the region.
Japan has said that a Chinese frigate last month locked weapons-control radar onto one of its destroyers on the high seas. It said another vessel had earlier targeted a helicopter, actions Prime Minister Shinzo Abe called "provocative" and "dangerous."
However, say analysts, Japan must walk a delicate diplomatic tight rope, with pressure to keep China onside as the wider world seeks Beijing's support for stricter sanctions on North Korea in the wake of its nuclear test.