The Chinese Foreign Ministry expressed "concern" over a fishery pact signed on Wednesday by Japan and Taiwan authorities regarding operations near waters off the Diaoyu Islands in the East China Sea.

Japan's Kyodo News Agency quoted unnamed sources as saying that the deal will allow trawlers from Taiwan to operate in part of an "exclusive economic zone" near the islands that was unilaterally defined by Japan.

Tokyo has long challenged China's sovereignty over the Diaoyu Islands, and China-Japan ties ran into a deadlock after the Japanese government illegally "nationalized" part of the islands last September.

Foreign Ministry spokesman Hong Lei told reporters that the government's position on Taiwan's external interactions and other issues is consistent and clear, and it expresses concern about the fishery agreement signed by organizations from Japan and Taiwan.

"We expect Tokyo to earnestly stick to its commitments on the one-China policy as well as the Taiwan question, and deal with Taiwan-related issues in a prudent manner," Hong said.

Feng Zhaokui, an expert at the Chinese Academy of Social Sciences, warned that it will be a serious issue if the pact labels Taiwan as a "country", a move that goes against Japan's previous commitments.

Japan has made promises to endorse the one-China policy in key bilateral political documents with China, including the China-Japan Joint Communique, which both countries signed on Sept 29, 1972, the year they normalized their diplomatic relations.

The Japanese government "fully understands and respects" the Chinese government's position that Taiwan is an inalienable part of the territory of the People's Republic of China, according to the Joint Communique.

For centuries, the waters off the islands have been a traditional fishery area for generations of Chinese fishermen.

But Japan has beefed up its claim in recent decades, and has long refused to recognize the previous political consensus between the two countries to shelve the islands dispute.

Cases were also reported of Japan illegally arresting Chinese fishermen who were operating in the waters off the islands, Feng Zhaokui said.

Fan Liqing, a spokeswoman for the Taiwan Affairs Office of the State Council, reiterated that the Diaoyu Islands and affiliated islets are China's inherent territory.

"It is the duty across the Straits to ensure the fishing rights and interest of fishermen from both sides (to operate) in this traditional fishery area on the basis of safeguarding territorial sovereignty," Fan told reporters on Wednesday.

China has enhanced maritime patrols around the islands since last September.

Chinese Marine Surveillance ships patrolled waters near the Diaoyu Islands on Tuesday, according to the State Oceanic Administration.

The signing of the fishery pact came after China made strong protests on March 11 over violations of the one-China policy related to Tokyo's commemoration of the devastating 2011 earthquake.

During the ceremony to mark the second anniversary of Japan's major earthquake and tsunami in 2011, Tokyo arranged that personnel from Taiwan would be part of a "diplomatic delegation".