Because of copyright issues regarding certain enemy characters (many of which were based on cultural icons) there were at least four versions of the game in Japan and North America, with the later two also appearing in Europe:
- Software revision 1.00 (1989)
- Enemy characters resembling Rambo called "Rocky", Jackie Chan, The Terminator called "Hercules" in Japan and "Master Attacker" in the West, Spider-Man, Batman, and Godzilla called "Monster-G" are present. Both Spider-Man and Batman are actually fake representations of the characters conducted by a shapeshifter named "Metamorpher" who alters his appearance after sustaining a certain amount of damage. Additionally, Joe Musashi's face on the title sequence resembled that of actor Sonny Chiba dressed as his character Hattori Hanzō from the Japanese TV series Shadow Warriors (Kage no Gundan).
- Software revision 1.01 (1989)
- The fake Spider-Man is now redesigned into the licensed character from Marvel Comics. Since he is now the real Spider-Man, he does not morph into Batman. Instead, Spider-Man leaves the battle when enough damage is inflicted and Batman is replaced by a winged Devilman-like creature. Monster-G remains unmodified. The "Gunner" enemy soldiers with flamethrowers are also changed to bald men with headbands, altering their original likeness to Rambo (although Sega had the license to the character for their Rambo III console games, they did not use it for this game).
- Software revision 1.02 (1990)
- A new copyright screen is made to acknowledge the license to Spider-Man (Sega already had the license to the character for their game The Amazing Spider-Man vs. The Kingpin) and the music composition by Yuzo Koshiro. Monster-G still remains intact.
- Software revision 1.03 (1990)
- Monster-G is redesigned into a skeletal dinosaur. Everything else remains intact from the previous revision, including the licensed use of Spider-Man. This version was used in the Genesis 6-Pak cartridge along with the "Sega Classics" edition of the game.
- Software revision 1.04 (2009/2012)
- Since the licensed use of the boss Spider-Man was for a limited period of time, the game was subsequently prevented from being re-released years later. The 2009 release for the Virtual Console as well as the Xbox Live Arcade and PlayStation Network 2012 releases feature a new software revision (1.04) that omits the Marvel copyright notice and replaces Spider-Man with a pink palette swap of the character that still behaves the same as the licensed Spider-Man. Joe Musashi's design in the title screen was also altered to remove his likeness to Sonny Chiba.
The credit roll, shown when achieving a "good" ending, was removed from the non-Japanese versions of the game. In versions 1.00 and 1.01, "©SEGA 1989 / MUSIC ©1989 YUZO KOSHIRO" would be shown at the bottom of the title screen like normal; when the Spider-Man copyright notice was added to the game, all copyright bylines were moved to a screen displayed before the intro.
Sega Smash Pack[edit]
The version included in volume 1 of the PC Smash Pack collection appears to be a prototype version. The internal ROM date says March 1989, and the product number is filled with zeroes. In the notes section of the ROM header (at 0x1C8), there is the string, "A0115 Sega_Channel", whereas all other releases have that area filled with ASCII space characters. The header is also only marked as being a Japanese release, while all other versions are marked as Japanese, US, and European.
The title screen always uses The Super Shinobi regardless of the console region. The game has an invincibility mode in the options screen, and a level select at the main menu. Enabling invincibility also gives infinite lives from falling offscreen, going out open doors, and using Mijin (it also prevents the player from gaining lives). There are other changes found in the options menu: the shuriken option is spelled "syurikin" (in other versions, it is spelled "shurikin"), and the sound test option lacks music titles, showing only a hex number (in other versions, sound effects are numbered in decimal).
There is no copyright screen. The introduction uses the final version Round 1 music (The Shinobi) instead of its own theme. The sound effect when Musashi changes his grip does not play, and the sparks when shuriken hit the sword stay on screen longer. There are no demos other than the opening animation (i.e. no plot text or gameplay demos).
Using Mijin uses up ninjutsu; in other versions, ninjutsu is still available after using Mijin. Mijin also remains selected after it has been used, instead of switching to Ikazuchi. There is also no shouting sound effect when ninjutsu are activated.
The final game has nineteen music tracks, but this version only has the first seven (the order of music in the sound test is unchanged). Because of this, there are differences in what music is used for what round, but even when the music is in all versions, different tracks are used. The music used in 1-1 is China Beat, and 1-2's music is "Make Me Dance" while, in the final version, both stages use The Shinobi. The game over screen has no music and is missing the Masked Ninja's laughter. The drum samples used throughout the game are also different.
For the most part, the enemies resemble the REV00 versions including the two-phase fight with Metamorpher, appearing as an imposter Spider-Man and Batman.
Some bosses appear incomplete. Monster-G, the boss of Round 7, seems to be invincible, and the fight ends after the boss goes through a few attacks. The Round 3 and 8 bosses appear to be missing completely (although the maps themselves are there); the game switches to the end of the level screen shortly after starting. There is no ending either: the game loops back to Round 1 after 8–3.