Tokyo branded as "very dangerous" a move by Beijing Saturday to set up an "air defence identification zone" over an area that includes disputed islands controlled by Japan, but claimed by China.

In a move that raised the temperature of a bitter territorial row between the two countries, China's defence ministry said that it was setting up the zone to "guard against potential air threats".

It later scrambled air force jets, including fighter planes, to carry out a patrol mission Saturday in the newly established zone.

The outline of the zone, which is shown on the Chinese defence ministry website and a state media Twitter account (pic.twitter.com/4a2vC6PH8O), covers a wide area of the East China Sea between South Korea and Taiwan that includes airspace above the Tokyo-controlled islands known as the Senkaku to Japan and Diaoyu to China.

Junichi Ihara, who heads the Japanese foreign ministry's Asian and Oceanian affairs bureau, lodged a protest by phone to Han Zhiqiang, minister at the Chinese Embassy in Japan, the ministry said in a statement.

He said Japan could "never accept the zone set up by China" as it includes the Tokyo-controlled islands, the statement said.

Ihara also told the Chinese side that such move by Beijing would "escalate" current bilateral tensions over the islands, branding it "very dangerous".

Japan's vice foreign minister Akitaka Saiki plans to summon the Chinese ambassador to Japan, Cheng Yonghua, as early as possible on Monday and state Japan's position on the matter, Kyodo news agency reported.

Chinese Defence Ministry spokesman Yang Yujun said the establishment of the zone, which became operational on Saturday morning, was aimed at "safeguarding state sovereignty, territorial land and air security, and maintaining flight order".

"It is a necessary measure in China's exercise of self-defence rights. It has no particular target and will not affect the freedom of flight in relevant airspace," Yang said in a statement on the ministry's website Saturday.

"China will take timely measures to deal with air threats and unidentified flying objects from the sea, including identification, monitoring, control and disposition, and it hopes all relevant sides positively cooperate and jointly maintain flying safety," he said.

Along with the creation of the zone in the East China Sea, the defence ministry released a set of aircraft identification rules that must be followed by all planes entering the area, under penalty of intervention by the military.

Aircraft are expected to provide their flight plan, clearly mark their nationality, and maintain two-way radio communication allowing them to "respond in a timely and accurate manner to the identification inquiries" from Chinese authorities.

Shen Jinke, spokesman for the People's Liberation Army Air Force, said late Saturday that it had conducted a patrol of the area using early warning aircraft and fighters.

"The patrol is in line with international common practices, and the normal flight of international flights will not be affected," Shen said.

Four Chinese coastguard boats briefly entered Senkaku waters on Friday, following multiple incursions at the end of October and start of November which revived tensions between Beijing and Tokyo.

Japanese Defence Minister Itsunori Onodera said in late October that the repeated incursions were a threat to peace and fell in a "'grey zone' (between) peacetime and an emergency situation".

He spoke after a report said Japan had drafted plans to shoot down foreign drones that encroach on its airspace if warnings to leave are ignored.

The Chinese defence minister warned Japan that any bid to shoot down its drones would constitute "an act of war".

Sino-Japanese relations have remained at a low-ebb for more than a year as a result of the dispute, which was revived when Japan nationalised three of the archipelago's five islands in September 2012.

Since that time, China has sent regular coast guard patrols to the islands, which are 200 kilometres (125 miles) northeast of Taiwan and 400 kilometres west of Japan's Okinawa.