Yaeyama was used by the Imperial Japanese Navy primarily as an aviso (dispatch boat) for scouting, reconnaissance and delivery of high priority messages.

With a small displacement, powerful engines, and a 20.75-knot (38.43 km/h) speed, the heavily armed and lightly armored Yaeyama was an example of the Jeune Ecole philosophy of naval warfare advocated by Bertin.

[2] Yaeyama was active in the First Sino-Japanese War, protecting troop transports to Korea, and covering the landing of Japanese forces at Port Arthur.

While operating in support of the invasion of Taiwan, Yaeyama precipitated a diplomatic incident with the United Kingdom when her captain intercepted the British-flagged merchant ship SS Thales in international waters on the morning of 21 October 1895.

Thales had departed Taiwan the previous day with 800 passengers en route to Amoy, including Liu Yongfu, the provisional second president of the Republic of Formosa and leader of the military resistance against the Japanese invasion.

The boarding party was unable to locate Liu (who had disguised himself as a coolie), but attempted to detain seven other Chinese passengers suspected of being part of the Formosa government.