After repairs at Kure, the ship remained in the Inland Sea without aircraft until 27 October when she was tasked to transport material to Borneo. On 3 November, she was attacked by the submarine , but her escorting destroyer, , deliberately sacrificed herself by intercepting the torpedoes and sank with no survivors. While returning from Manila, "Jun'yō" was attacked by the submarines , and early in the morning of 9 December 1944. She was hit by three torpedoes, but she was able to proceed on one engine. She reached Sasebo the following day and began repairs on 18 December.