It was intended to be used with the I-400, a 4500-ton submarine dubbed a "submersible aircraft carrier". Two to three of the craft would be stowed aboard in disassembled form, and launched by catapult. The twin floats could be jettisonned, and the aircraft was essentially meant to be ditched at sea upon completion of its mission.
An alternate version with landing gear instead of floats was designated M6A1-K and named Nanzan (南山, "Southern Mountain"). While generally described as a land-based trainer, some sources indicate that it was designed for the attack role, to be launched from the submarine and then landed. Besides the difference in landing gear, the Nanzan's vertical stabilizer was clipped to balance out the weight.
The first M6A1 was completed in November 1943, and 28 examples (including M6A1-Ks) were completed by 1945. The type was never used in service. A single M6A1 has been preserved and resides at the National Air and Space Museum in Washington, DC.
One Aichi AE1P Atsuta 30 or Atsuta 31 twelve-cylinder inverted-vee liquid-cooled engine, rated at 1,400 hp for take-off, 1,250 hp at 1,700 m and 1,290 hp at 5,000 m, driving a constant-speed three-blade metal propeller (M6A1 prototypes).
One Aichi Atsuta 32 twelve-cylinder inverted-vee liquid-cooled engine, rated at 1,400 hp for take-off, 1,340 hp at 1,700 m and 1,290 hp at 5,000 m, driving a constant-speed three-blade metal propeller (M6A1 production aircraft and M6A1-K prototypes).
One Mitsubishi MK8P Kinsei 62 fourteen-cylinder air-cooled radial, rated at 1,560 hp for take-off, 1,340 hp at 2,100 m and 1,190 hp at 5,800 m, driving a three-blade constant-speed metal propeller (E16A2 prototype).