Originally the developers of The Revenge of Shinobi intended Joe Musashi's master (the old man dying in the intro) to reveal himself to be the head of Neo Zeed and to be the game's true final boss. In addition to his martial arts skills, he would also have been able to summon earthquakes and falling rocks. The entire battle was sequenced and designed, but due to time constraints it never made it into the final game.

The Japanese version of the game was renamed "The Super Shinobi". Putting a US copy of the game into a Japanese console will still show the title as The Super Shinobi. Likewise, playing a Japanese copy of the game on a American or European machine will still show the title as Revenge of Shinobi.

In the original release, Batman and Spiderman appear as bosses. Batman was later replaced by a different enemy, while SEGA added a copyright disclaimer for Marvel Comics, who allowed Spiderman to stay in the game.