During the Japanese invasion the Philippines, she returned to her home port of Manila where the Asiatic Fleet had retreated. On 27 December 1941, Japanese attack planes from the 1st Kōkūtai and the Takao Kōkūtai attacked Manila Bay[4] setting Arayat, her fellow customs cutter Mindoro, and the motor vessel Ethel Edwards ablaze while also sinking the lighthouse tender Canlaon outright, and so heavily damaging the steamship Taurus, her crew was forced to scuttle her.[4]
On 5 October 1944, she left Miri along with Type D escort shipsCD-18 and CD-26 providing escort for Myogi Maru, Heian Maru, Mikasa Maru, and Teiyu Maru (ex-Carignano) headed for Manila.[5] The convoy was carrying supplies for the besieged forces on Leyte Island. The convoy arrived safely at Manila on 2 November 1944. On 27 November 1944, she departed Manila as part of convoy TA-6 with No.28-classsubmarine chasersCH-45 and CH-53 and freighters Shinsho Maru and Shinetsu Maru.[5] On 28 November 1944, the convoy arrived safely at Ormoc Bay, Leyte.[5] The three escorts were assigned to guard the entrance to the harbor while the transports unloaded.[5] They were soon confronted by American PT boats, PT-127 and PT-331 who each launched 4 torpedoes sinking CH-53 at (10°59′N124°33′E / 10.983°N 124.550°E / 10.983; 124.550) and heavily damaging PB-105 which was run aground and abandoned (the Americans capture her hulk on 8 December 1944).[5] The transports were able to unload their much-needed supplies although after departing, Shinetsu Maru and CH-45 were sunk by American planes on 29 November 1944 and Shinsho Maru met the same fate on 30 November 1944.[8]
On 10 January 1945, PB-105 was struck from the Naval List.[5]