On 15 March 1889, "Nipsic" rode at anchor in Apia Harbour with , , , and three German naval vessels, SMS "Adler", "SMS Olga", and SMS "Eber", along with six merchantmen. Gale-force winds arose, and preparations for leaving harbor were begun, but departure was delayed in the hope that conditions next morning would be more favorable for the sortie. However, by early morning on 16 March the harbor was a mass of foam and spray as hurricane-force winds battered the ships in the 1889 Apia cyclone. Only "Calliope", larger and more strongly powered than the others, was able to leave the harbor. "Vandalia", "Trenton", "Adler" and "Eber", and the merchantmen were all sunk; "Nipsic's" captain, Cmdr. D. W. Mullin, was able by superb seamanship to beach his ship. While severely damaged by the pounding she received on the beach, "Nipsic's" hull was intact, although much of her topside structure was battered, all of her propeller blades damaged, two boilers spread and useless, and eight of her crew lost. Refloated and her engines repaired, "Nipsic" cleared Apia on 9 May for Auckland, but was turned back by heavy seas. On 15 May she again sailed, for Pago Pago, Fanning Island, and Honolulu, arriving on 2 August.