On 10 May 1895, he was promoted to full admiral and became the first Japanese Governor-General of Taiwan, being responsible for moving the seat of government to Taipei.
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It states something of his personality to note that he ordered his flagship, the lightly armed passenger liner Saikyo to charge the Chinese fleet at the Battle of the Yalu River.
Transferred to the converted passenger liner Saikyo-maru, Yamaya served as chief navigator during the First Sino-Japanese War and was present during the Battle of the Yalu on September 17, 1894, along with the belligerent Navy General Staff Admiral Kabayama Sukenori.