Japanese Army Naming Conventions

The Japanese Army used a combination of methods in their naming of aircraft. The system consisted of a Kitai or airframe numbering system that began in 1932 and remained in use thoughout the war. Also some of the aircraft received a "popular name". Research aircraft, gliders and rotary wing aircraft were given special designations. Also, any aircraft that was built previous to 1932, but still in service at the time of implementation of the new Kitai system were also included in the airframe numbering system. These Kitai numbers were assigned in numerical order until 1944 when the Japanese tried to confuse allied intelligence by assigning numbers in a less sequential order.

Models with the same airframe kept the same Ki number and were differenciated by a roman numeral to show a change in model. Different versions of the same models received an additional Japanese characters. These consisted of Ko, Hei, Otsu and sometimes supplemented by a Kaizo or Kai.

An example of the Ki-61 Tony, taken from Rene' Francillon's book called Japanese Aircraft of the Pacific War (you gotta buy this book!)

Ki-61 Designation of the project and prototypes.
Ki-61-Ia First production version of the first model.
Ki-61-Ib Second production version of the first model.
Ki-61-I KAIc Third production version of the first model
Ki-61-I KAId Fourth production version of the first model
Ki-61-II Prototypes of the second model
Ki-61-II KAI Modified prototypes of the second model
Ki-61-II KAIa First production version of the second model
Ki-61-II KAIb Second production version of the second model.
Ki-61-III Projected third model.

Gliders initially worked under this system, but were later moved to Guraida (Ku) numbers.

References:
1) Japanese Aircraft of the Pacific War by Rene' J. Francillon. Putnam Aeronautical Books, 1970