He warned that the confrontation could lead to conflict that would damage the regional and world economies.
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Japan's Chief Cabinet Secretary Yoshihide Suga told reporters on Thursday that Japan - which is also involved in a territorial dispute with Beijing over East China Sea islands - was "strongly concerned about heightened tensions in the region due to China's illegal exploration".
"We urge [China] to refrain from taking unilateral actions that would escalate the tensions, and exercise restraint in accordance with international law," Mr Suga said, according to the Japanese news agency Kyodo.
China claims a U-shaped swathe in the South China Sea that overlaps areas claimed by several of its neighbours.
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The Philippines is currently taking China to the UN court over maritime territorial disputes.
On Wednesday, Philippine police seized a Chinese fishing boat and detained its 11 crew in another disputed part of the South China Sea, prompting a protest from China.
China has called for the immediate release of the fishermen and their boat.
Foreign ministry spokeswoman Hua Chunying warned the Philippines to "make rational explanations" and "take no more provocative action".
She added that a Chinese maritime police boat had arrived in the area.
The Philippines said the fishermen would be investigated to see if they broke the law, including one on endangered species. Several hundred turtles were reportedly found in their boat.
National Police Chief Alan Purisima told media the fishermen's arrest was made in Philippine territory.
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