Lieutenant General Qi Jianguo, deputy chief of staff of the People's Liberation Army, told a security conference in Singapore that the scholars' views did not represent the official position.
The People's Daily, China's most circulated newspaper, had published an article last month written by two scholars from a top state-run think-tank that argued Beijing may have rights to the Ryukyus.
The lengthy article argued that the island chain was a "vassal state" of China before Japan annexed it in the late 1800s.
However, he repeated Chinese arguments for China's historical claims over a set of tiny uninhabited islets in the East China Sea known as the Diaoyus in China and Senkakus in Japan.
"I have to say Diaoyu islands and Ryukyu islands and Okinawa islands... The first, and the second and the third, are not the same nature. The Chinese government on this is very clear," he said.
The two nations have stepped up a war of words in recent months, with Chinese vessels regularly entering waters around the islands, stoking fears of armed conflict.
Some Chinese see historical ties as a basis of sovereignty and dismiss Japan's possession of the islands as a legacy of its aggressive expansionism that ended in defeat at the end of World War II.
Before being annexed into Japan in the late 19th century, the independent Ryukyu kingdom, centred on Okinawa, paid tribute to China for centuries -- as did numerous other traditional Asian states -- often receiving favourable trading rights in return.