China told Japan Wednesday to respect its "indisputable sovereignty" over islands claimed by both countries in the East China Sea, in the latest territorial row between Beijing and its neighbours.

Chinese Foreign Minister Yang Jiechi met Japanese counterpart Koichiro Gemba in Phnom Penh where he "reaffirmed China's principled position" on the islands known as Senkaku in Japanese and Diaoyu in Chinese.

"He stressed that Diaoyu Islands and their affiliated islets have always been China's territory since ancient times, over which China has indisputable sovereignty," said a statement from the Chinese delegation.

Japan summoned the Chinese ambassador in Tokyo as three Chinese patrol boats approached the chain of islands, which are privately held by Japanese owners.

The crew of the Chinese vessels, which have since left the islands' immediate vicinity, initially rebuffed Japanese orders to leave, Japanese officials said.

"We are conducting official duty in Chinese waters. Do not interfere. Leave China's territorial waters," the Chinese crews said, according to the Japanese coastguard.

The waters around the disputed islands, which are close to oil reserves, have been the scene of previous rows, including the arrest of a Chinese trawlerman in late 2010.

Wednesday's spat is the latest clash over disputed territory between China and its neighbours that threatens to overshadow attempts to smooth regional relations at an Asian security summit in Cambodia this week.

The 10 members of Southeast Asian regional body ASEAN have been trying to agree a long-stalled "code of conduct" for the South China Sea that would help settle overlapping claims in the resource-rich waterway.

The Philippines is leading a push for ASEAN to unite to persuade China to accept a code based on a UN law on maritime boundaries that would delineate the areas belonging to each country.

Manila also wants ASEAN to condemn a standoff last month between Philippine and Chinese ships over Scarborough Shoal, an outcrop in the South China Sea.

Yang urged Japan to adhere to agreements and understandings with China "in good faith" and said it should return to "the right path of managing differences through dialogue and consultation with the Chinese side."

Japan-China relations this year had seen "some acute problems", the Chinese foreign minister acknowledged.

China's assertiveness over disputed territories in the South China Sea, which is home to vital shipping lanes, is seen by analysts as pushing anxious neighbouring countries closer to the United States.

Beijing also recently angered Vietnam by inviting bids for exploration of oil blocks in contested waters, sparking protests in Hanoi.

US Secretary of State Hillary Clinton arrived in Cambodia on Wednesday to press for closer relations with ASEAN, part of Washington's strategy of "pivoting" towards Asia to challenge China's influence.

She is to take part in the ASEAN Regional Forum on Thursday, which brings together 26 nations and the European Union.