The specification demanded an endurance of six hours and sufficient speed to evade interception by any fighter in existence or development, but otherwise did not constrain the design by a team led by Tomio Kubo and Jojo Hattori.

It had a small diameter oval fuselage which accommodated a crew of two, with the pilot and observer situated in individual cockpits separated by a large fuel tank.

The engines, two Mitsubishi Ha-26s, were housed in close fitting cowlings developed by the Aeronautical Research Institute of the Tokyo Imperial University to reduce drag and improve pilot view.

[8] During operational testing in March 1944, it was discovered that replacing the engines' single exhaust collector ring with individual pipes provided extra thrust and an increase in top speed to 642 km/h (399 mph).

Wittridge had removed two machine guns and the seat armour and also polished the wing leading edges to gain extra speed.

[13] The leading American fighter pilot Richard Bong, flying a P-38 Lightning, managed to shoot down a Ki-46 over the coast of Papua New Guinea in late 1942.

The Ki-46 was also assigned to two whole Sentai (wings/groups), as well as individual Chutaicho (junior operational commanders) in the Imperial Japanese Army Air Service, during the Pacific War.

The only complete survivor is a Ki-46-III Army Type 100 example, that is part of the collection of the Royal Air Force Museum in the United Kingdom.

[15] In late 1945, Japanese Surrendered Personnel at Kuruan Airfield in British Malaya were ordered to restore two Ki-46's at the base to airworthy condition for the Allied Technical Air Intelligence Unit.

[15] It became part of the RAF St Athan collection of historic aircraft, before moving to the Royal Air Force Museum Cosford in 1989.