On the morning of 4 October, she attacked a destroyer, then survived an intensive depth charge attack with seemingly minor damage. When she submerged the next day, however, the submarine began taking water. She surfaced, made repairs, then submerged to . Leaks were found in her motor room and torpedo room flappers. The latter were jacked shut, but the former continued spraying water onto both motors. Within an hour, four Japanese destroyers had moved into the area. "S-44" went to . The leak worsened. The motors were covered in canvas and sheet rubber and the crew waited for the destroyers to pass over her position. As they disappeared, "S-44" moved up to and repairs were made on the flapper. That night, further repairs were made while the ship was surfaced off Santa Isabel Island; and, by midnight, the S-boat was en route back to her patrol area. On 7 October, bad weather set in; and, on 8 October, she departed the area, arriving in Moreton Bay on 14 October.