At the time of the attack on Pearl Harbor in December 1941, "Yaeyama" was assigned to “Operation M” (the invasion of the southern Philippines) deploying from Palau to mine the Surigao Strait. On 3 January 1942, she became flagship for Admiral Rokuzo Sugiyama’s Third Southern Expeditionary Fleet and covered landings at Subic Bay. While at Subic May on 1 February, she was attacked unsuccessfully by USS "PT-32". "Yaeyama" was based at Manila from July 1942 under the overall command of the Southwest Area Fleet.