She was part of the fleet that landed troops during the Hainan Island Operation on 9 February 1939. She was anchored at Cam Ranh Bay, French Indochina, with Imperial Japanese Navy forces in preparation for the Japanese invasion of Malaysia in December 1941. On 9 July 1942, she landed 250 members of the Hara Construction Force and security troops on Guadalcanal to help build Lunga Airfield, and then transported 50 more men to Gavutu to build installations.
After heading back under her own power to Lae, she was quickly patched up to return the following day to offload the much-needed equipment. On 30 July, under the protection of the light cruiserTatsuta and destroyerYūzuki, she headed back to Buna at 1330. En route she was attacked by Allied aircraft at around 1515. Later she came under attack by eight B-17 Flying Fortresses of the USAAF 19th Bombardment Group and was hit by at least three 500-pound (227-kg) bombs at 1640 and was disabled. Her crew abandoned ship, and Tatsuta and Yūzuki rescued the survivors and steamed to Rabaul.
The unmanned Kōtoku Maru remained afloat and adrift and ran aground near Salamaua at 07°01′N147°07′E / 7.017°N 147.117°E / 7.017; 147.117. The Japanese undertook salvage on her wreck, removing some of her cargo. After the Allies occupied Salamaua, they salvaged winches and other gear from her wreck on 15 July 1944. The ship remained upright until sometime after 1945, when she rolled over onto her side.