The People's Daily, the mouthpiece of the ruling Communist Party, yesterday published a call for a review of Japan's sovereignty over Okinawa, suggesting that Beijing may be the rightful owner.
The call came as the two countries are already at loggerheads over islands in the East China Sea.
"We have protested both in Tokyo and Beijing over the commentary issued by the People's Daily, followed by a Chinese foreign ministry comment," a Japanese foreign ministry official in charge of Chinese affairs told AFP.
"The Chinese side replied to us that the view in the commentary was solely held by researchers," he added.
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The lengthy article in the People's Daily argued that the country may have rights to the Ryukyu chain, which includes Okinawa.
Okinawa is home to major US air force and marine bases as well as 1.3 million people, nearly all of whom are Japanese nationals and speak Japanese.
The authors of the article, two scholars at the Chinese Academy of Social Sciences, considered China's top state-run think-tank, said the Ryukyus were a "vassal state" of China before Japan annexed the islands in the late 1800s.
The article also repeated Chinese government arguments for China's historical claims over a set of tiny uninhabited islets known as Diaoyu in Chinese and Senkaku in Japanese, over which the two sides are squabbling.
Following the article, the Chinese foreign ministry reportedly said "the history of Ryukyu and Okinawa has long called for attention in academia".
The two nations have stepped up a war of words on the Senkakus in recent months, with Beijing's vessels regularly entering the waters around the Tokyo-controlled islands, stoking fears of armed conflict.