I-54 departed Yokosuka on 7 July 1944, bound for Saipan towing an Unpoto gun carrier,[1] a 70-foot (21.3 m) sled that could carry up to 15 tons of cargo, usually in the form of three Type 96 15-centimeter (5.9 in) howitzers and ammunition for them.[2]Fleet Radio Unit, Melbourne (FRUMEL), an Alliedsignals intelligence unit headquartered in Melbourne, Australia, intercepted and decrypted a Japanese message that day stating that I-54 was due to arrive at Tinian on 14 July 1944 to evacuate Imperial Japanese Navy Air Service personnel.[1] Saipan fell to American forces on 9 July 1944, and I-54 was ordered to nearby Tinian that day.[1] She lost her Unpoto sled in heavy seas.[1] On 10 July 1944, she was reassigned to Submarine Division 15 in the 6th Fleet.[1] On 15 July, FRUMEL intercepted and decrypted another Japanese message saying that I-54 was scheduled to arrive at Tinian on 18 July.[1] She returned to Yokosuka on 24 July 1944.[1]
On 18 October 1944, I-54 received orders from the 6th Fleet to join 12 other submarines in patrolling east of Leyte in the Philippines.[1]I-54 was assigned a patrol area 120 nautical miles (220 km; 140 mi) east of the Philippines between the areas assigned to the submarines I-38 and I-46, and she was expected to arrive in her patrol area on 25 October 1944.[1]
The Battle of Leyte began with the U.S. landings on Leyte on 20 October 1944, and that day I-54 acknowledged an order to change her patrol area. She transmitted another message on 23 October 1944, the first day of the Battle of Leyte Gulf of 23–26 October 1944.[1] The Japanese never heard from her again.[1]
On both 30 October and 1 November 1944, I-26, I-46, and I-54 all failed to make scheduled daily 19:00 status reports.[3] On 20 November 1944, the Imperial Japanese Navy declared I-54 to be presumed lost east of the Philippines with the loss of all 107 men on board.[1] She was stricken from the Navy list on 10 March 1945.[1]
The identity of the submarine Gridley and Helm sank remains a mystery, and has been reported both as I-46 and I-54.[1][3] Some sources have credited the destroyer escortUSS Richard M. Rowell (DE-403) with sinking I-54 in the Philippine Sea on 26 October 1944 while screening Task Group 77.4, although the submarine Richard M. Rowell attacked probably was I-56, which survived.[1]