The first attempt to replace the venerable Ki-21 bomber resulted in the Nakajima Ki-49 Donryu (Storm Dragon). It proved rather disappointing in service with performance figures little (if at all) better than its predecessor, and with a crew of eight was very inefficient in manpower. Although it included armor protection and self-sealing fuel tanks, inadequate defensive armament in the early variants made it easy prey for Allied fighters. This flaw was subsequently improved but the Ki-49 never truly replaced the 'Sally' and ended the war fulfilling maritime patrol (with ASV radar), anti-submarine warfare (with magnetic anomaly detectors), night fighter, and transport tasks as well as being used as suicide bombers. The Ki-49's main area of operations was the South Pacific and the Philippines but it will be remembered mostly because of its participation in the famous 1942 raid on Port Darwin, Australia; its first combat mission of the war.

First flown in August 1939, the Ki-49-I entered service two years later with the intention of replacing the Ki-21. Performance was mediocre so additional armament as well as upgraded Ha-109 engines (replacing Ha-41s) resulted in the Ki-49-II which entered service in 1942 and became the most widely produced variant (the Ki-49-IIa and -IIb subvariants had various defensive armament configurations). Futher modifications led to the Ki-49-III prototype with improved engines as well as the Ki-58 heavy fighter and the Ki-80 formation lead ship. Additional conversions included MAD-equipped anti-submarine aircraft and night fighters armed with a 75-mm cannon.