In the Second World War the Imperial Japanese Navy used her first as a submarine depot ship and then to transport aircraft.

Ishihara Sangyo Kaiun Goshi Kaisha (ISK) is a Japanese company that had mines in Malaya and operated a fleet of cargo ships.

[4] In October 1943 the submarine USS Silversides sank Johore Maru in the Pacific Ocean northwest of the Bismarck Archipelago.

[4] On 31 December 1943, the submarine USS Herring sighted a convoy off the Japanese coast that included Nagoya Maru.

The next day, 1 January 1944, Herring sank Nagoya Maru by torpedo[7] off the island of Aogashima at position 35°15′N 138°02′E / 35.250°N 138.033°E / 35.250; 138.033, killing 110 passengers and one member of the ship's crew.