John Liu originally shot the film in 1984 in New York City. The film remained unfinished until Vinegar Syndrome found the original unedited camera negative in their film archive. With the sound elements and script lost, producer/editor Kurtis Spieler finished the film and hired a new cast to dub the voices as well as the band Voyag3r to create an original score.
Contrary to early reports, a lipreader was not brought in to assist with the dubbing. Because the movie was unedited, a lipreader would have had to read the lips for every take of the movie. Instead, editor Kurtis Spieler cut the movie together first and then wrote new dialogue to match the performances of the actors. The result is similar to a foreign film where the words do not always match the mouth movements of the actors. This was done to create a more coherent story and add to the fun of the film.
Most of the on-screen cast list remain unidentified as of 2023 because no production records are known to survive.
The film Ninja III: The Domination (1984) can be seen advertised on a movie theatre marquee at one point.