Following a shipwreck of a Ryukyuan vessel on the southeastern tip of Taiwan in winter of 1871, in which the heads of 54 crew members were taken by the aboriginal Taiwanese Paiwan people in Mutan village (牡丹社), the Japanese sought to use this incident as a pretext to formally annex the Ryukyu Kingdom as a Japanese prefecture (Frederic 2002) and expand into Taiwan. According to records from Japanese documents, Mao Changxi (毛昶熙) and Dong Xun (董恂), the Chinese (Qing) ministers at Zongli Yamen (總理衙門) who handled the complaints from Japanese envoy Yanagihara Sakimitsu (柳原前光) replied first that they had heard only of a massacre of Ryukyuans, not of Japanese, and quickly noted that Ryukyu was under Chinese suzerainty, therefore this issue was not Japan's business. In addition, the governor-general of the Qing province Fujian had rescued the survivors of the massacre and returned them safely to Ryukyu. The Qing authorities explained that there were two kinds of aborigines on Taiwan: those governed by the Qing, and those unnaturalized "raw barbarians... beyond the reach of Qing government and customs." They indirectly hinted that foreigners traveling in those areas settled by indigenous people must exercise caution. After the Yanagihara-Yamen interview, the Japanese said that the Qing government had not opposed Japan's claims to sovereignty over the Ryukyu Islands, disclaimed any jurisdiction over Aboriginal Taiwanese, and had indeed consented to Japan's expedition to Taiwan; however, these claims were unfounded (Leung 983:270).

The Qing Dynasty made it clear to the Japanese that Taiwan was definitely within Qing jurisdiction, even though part of that island's aboriginal population was not yet under the influence of Chinese culture. The Qing also pointed to similar cases all over the world where an aboriginal population within a national boundary was not under the influence of the dominant culture of that country.

The Japanese nevertheless launched an expedition with a force of 2000 soldiers in 1874. The number of casualties for the Paiwan was about 30, and that for the Japanese was 543 (12 Japanese soldiers were killed in battle and 531 by disease). Eventually, the Japanese withdrew as about Qing Dynasty sent 3 divisions of forces (9000 soldiers) to reinforce Taiwan. The Okinawan affair was more of a trial balloon sent up by the Japanese to test the situation on Taiwan for a possible colonization campaign of their own. This caused the Qing to re-think the importance of Taiwan in their maritime defense strategy and greater importance was placed on gaining control over the wilderness regions.

Reference

http://en.wikipedia.org/wiki/History_of_Taiwan