Japan said Friday it was monitoring waters near islands disputed with China in the East China Sea after it spotted a naval intelligence ship from the country operating in a new area for the first time.

Japan's Defence Ministry said late Thursday a P-3C patrol aircraft observed the Dongdiao-class intelligence vessel near territorial waters of the Senkaku Islands, which Japan administers but China claims as the Diaoyus.

The ship repeatedly moved back and forth in the area until Thursday evening before departing, never breaching Japan's 12-nautical-mile territorial waters, the ministry statement said.

Japanese defence minister Gen Nakatani called the ship's moves "unusual" at a regular press conference Friday, saying it made "repeated eastward and westward moves in one day".

The defence ministry will keep up monitoring of the Chinese navy and "make utmost efforts in patrolling the sea and air surrounding Japan", Nakatani said.

In Beijing, the Chinese government defended the ship's operations as standard.

"The Chinese naval vessel is conducting normal activities," spokesman Hong Lei told a regular briefing.

"It is in line with international law," he added. "There is nothing disputable about that."

Japan and China have routinely butted heads over ownership of the uninhabited islets, as Chinese state ships -- mostly coast guard -- and aircraft have approached them on and off to back up Beijing's claims and test Japan's response.

Relations between Japan and China hit multi-year lows after the Japanese government in September 2012 moved to increase its formal control by nationalising some of the islands.

But China and Japan -- Asia's two biggest economies, respectively -- have taken steps to improve ties.

They issued carefully worded statements on the dispute ahead of a summit last year in Beijing between Chinese President Xi Jinping and Japan's Prime Minister Shinzo Abe.

The two sides basically acknowledged they had different views on tensions emanating from the issue but agreed on the need for keeping them under control.

Distrust, however, remains high as China is wary of moves by Abe to raise Japan's military profile while Tokyo frets about Beijing's increasing regional and global assertiveness.

The latest move marked the first time a Chinese naval ship operated in the area between the disputed islands and the populated southern Japanese island of Miyako, a defence ministry spokeswoman earlier told AFP.

Nakatani himself declined to comment on the ship's aims but stressed that the Chinese military "is rapidly boosting their activities at sea and in the air".

Japan assumes that China "will try to expand the area of its activities further in the future", Nakatani added.

The 6,000-tonne vessel is armed with one 37 millimetre and two dual 14.5 millimetre cannons, the ministry said, citing IHS consultancy group's Jane's Fighting Ships site.

The mass circulation Yomiuri Shimbun daily reported that Japan will strengthen border security as a result of the spotting.

Anonymous sources from the ministry told the Asahi Shimbun newspaper the Chinese ship may have been there on an intelligence mission ahead of a planned drill this month by Japan's naval forces.