- Sentais: 61st, 62nd, 74th, 95th, 110th
- Hikoshidan: 11th
- Hamamatsu Army Heavy Bomber Flying School
First Sentai Equipped
The 14th Sentai was first equipped with the Ki-49.
The 61st Sentai was first equipped with the Ki-49-I in December 1941.
The Ki-49 equipped units used them in raids in China, New Guinea, and over Australia's Northwest Territory. The first raid on Darwin, Australia occurred on February 19, 1942.
Poor performance and heavy losses had the Ki-49 modified to have a magnetic anomaly detection (MAD) equipment for hunting submarines.
In the summer of 1942 the 7th and 61st Sentais were equipped with Ki-49-IIas and Ki-49-IIbs. Participated in attacks on Chungking and General C. L. Chennault's China Air Task Force bases.
The 12th Sentai used Ki-49s against Burma, eastern India, and Calcutta.
During the last year of the war the Ki-49s were used as night fighters, transports, and in suicide attacks at Mindoro in December 1944.