A Chinese naval ship sailed into waters surrounding disputed East China Sea islands for the first time early Thursday, prompting Tokyo to summon the Chinese ambassador to protest, the Japanese government said.

Russian naval ships were also seen in the area around the same time.

A Chinese naval vessel entered waters surrounding the Tokyo-administered isles, called Senkaku in Japan and also claimed as the Diaoyu islands by China, around 00:50 am (1550 GMT Wednesday), according to the Japanese foreign ministry.

It was a 3,963-ton Jiangkai class frigate, spotted by Japan's guided-missile destroyer Setogiri, the Japanese defence ministry said.

Contiguous waters are a 12-nautical-mile band that extends beyond territorial waters. Under international rules, they are not the preserve of any single country, although the resident power has certain limited rights.

"The fact that (China) sent a naval ship to the contiguous waters of our Senkaku Islands for the first time is an act that unilaterally increases tension and our nation is gravely concerned," Chief Cabinet Secretary Yoshihide Suga told a regular briefing.

Relations between Japan and China deteriorated in 2012 when Tokyo "nationalised" some of the islets.

Since then, the two largest Asian economies have taken gradual steps to mend fences but relations remain tense.

Japanese Vice Foreign Minister Akitaka Saiki summoned Chinese ambassador Cheng Yonghua around 2:00 am to lodge a protest.

Saiki "expressed grave concerns and protested, while demanding the ship immediately leave our nation's contiguous zone," the ministry statement said.

During his meeting with Saiki, Cheng claimed the Chinese frigate was allowed to sail in the waters, Kyodo News said, citing an unnamed source.

The frigate left the zone at about 3:10 am, the Japanese government said.

Japan's Defence Minister Gen Nakatani, who was visiting Thailand, told Japanese journalists that Tokyo was taking a measured response.

"We will continue our calm handling of this issue so as not to unnecessarily escalate the situation," Nakatani said in an televised group interview.

"We will continue to act firmly in order to defend our territorial land, waters and air space," he said.

Chinese coast guard vessels routinely travel around the disputed islands.

Three Russian military vessels were also seen in the waters around the disputed islands around the same time, a Japanese defence official said.

The Russian ships entered the area around 9:50 pm Wednesday and left around 3:05 am Thursday, he said.

Suga said Japan was analysing whether the Chinese and Russian moves were in anyway related.

But he added that a lack of territorial disputes with Russia in the regional waters made its moves less concerning.