Japan Thursday lodged an official protest with China, after it spotted a Chinese frigate in waters surrounding flashpoint islands in the East China Sea, the first such incursion in more than a year.

Japan's vice minister for foreign affairs Shinsuke Sugiyama summoned Chinese ambassador Cheng Yonghua to voice Tokyo's concerns, as the two Asian giants explore ways to ease bilateral tensions, complicated by North Korea's nuclear and missile drive.

Sugiyama "issued a protest by expressing serious concerns and strongly requested China not to interfere with the flow of improving Japan-China relations," the foreign ministry in Tokyo said in a statement.

Japanese navy ships spotted the 4,000-tonne Jiangkai II class frigate around 11:00 am (0200 GMT) in waters surrounding the Tokyo-administered isles, called Senkaku in Japan and also claimed as the Diaoyu islands by China.

In Beijing, foreign ministry spokesman Lu Kang told a regular press briefing "the Chinese naval vessels conducted surveillance over the activities of the Japanese side" and repeated China's claim to the islands.

Japanese defence ministry spokesman Go Yamaguchi told AFP that a submarine of unknown nationality had also been spotted entering the contiguous waters off the disputed islands.

"We are monitoring the vessels and sending a message to them that they entered the contiguous waters near Japanese territory," said Yamaguchi.

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 official told AFP it was the first such incursion since June 2016.

The warship and the submarine had left the waters by the afternoon, the defence ministry said in a statement.

Japan was monitoring the submarine, but would refrain from releasing details, including its identity, Japan's Chief Cabinet Secretary Yoshihide Suga told a regular briefing.

"We are dealing with this firmly and calmly," he said, stressing that Japanese and Chinese leaders have pledged to improve bilateral ties.

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

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

Chinese coastguard vessels routinely travel around the disputed islands.

The incident came as Japan is pushing to host a trilateral summit with leaders from China and South Korea.

Japan has also urged China to play greater roles in easing tension related to North Korea's missile and nuclear programmes.

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