Japan's government has made a formal protest to Beijing after two Chinese fisheries patrol boats were seen near a disputed island chain.
Relations between Asia's two biggest economies have been tense since a Chinese trawler captain was arrested by Japan's coastguard in the same area in early September.
The Chinese boats were spotted by the coastguard late on Sunday.
Protests over the territorial row took place in both countries at the weekend.
The islands in the East China Sea, known in Japan as Senkaku and in China as Diaoyu, are controlled by Japan, but claimed by China.
They are uninhabited, but surrounded by rich fishing grounds and potentially significant oil and gas reserves.
"Last night around 9pm (1200 GMT) our coastguard sighted them and afterwards the two (Chinese ships) left there and sailed north toward China," top Japanese government spokesman Yoshito Sengoku said.
"After the incident we launched a protest through diplomatic channels."
Japan and China have been locked in their worst dispute for years over the territorial issue.
It began when a Chinese trawler captain was arrested near the islands by Japan's coastguard in early September after colliding with two Japanese patrol boats.
The row has sparked nationalist protests in both countries.
On Sunday, about 200 people took part in anti-Japanese protests in Lanzhou in northwest China, a day after a similar protest in Deyang in the southwest.
In Japan, 300 anti-China protesters rallied in Takamatsu city on Saturday.
Meanwhile Japan has urged China to normalise customs inspections of exports of rare earths, used to make everything from wind turbines to hybrid cars.
Japanese trading houses have complained shipments have been disrupted since the row began.
China, which has a near monopoly on rare earths, has insisted there is no embargo in place.