Japan suspects China now has seven drilling rigs in operation out of 16 it has positioned in the disputed waters, officials said, the latest twist in a row over gasfields in waters claimed by the two countries.
"We are protesting with the Chinese side through a diplomatic channel," Chief Cabinet Secretary Yoshihide Suga told a news conference.
"It is extremely regrettable that the Chinese side... Has unilaterally gone ahead with the development while the border has not yet been settled," Suga said.
"China needs to abandon its unique obsolete argument, that no other countries adopt, that no international rulings have admitted -- that its rights extend along the continental shelf" to near Japan's southern Okinawa islet chain, a senior foreign ministry official told reporters on condition of anonymity.
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China is also embroiled in a separate row with Japan over disputed islands elsewhere in the East China Sea.
The islands are controlled by Tokyo, which calls them the Senkakus, which Beijing claims them as the Diaoyus. Chinese ships and aircraft regularly test Japanese forces in the area.