Tecmo held a poll on their website to let fans vote on which console they wanted to see the next Ninja Gaiden game on.

The game was released as an Xbox exclusive.
Most fans actually voted for the GameCube.

Though the game can run at 60 frames per second, the team had to lower the framerate to 30 frames per second when using Ninpo attacks due to hardware limitations. This change came to the disappointment of director Tomonobu Itagaki who strongly believed a ninja's magic should be "impressive and powerful" and who wanted the development team to use every resource they had to make the Ninpo attacks live up to his vision.

The first stage of development was to create the game on the Sega NAOMI arcade system. They then planned to move the project to the Dreamcast console for further development and release, but this was abandoned when Sega ended the console's production in 2001. The game was then planned to be a launch title for the PlayStation 2. However, the game's producer, Tomonobu Itagaki, changed the development towards an Xbox exclusive after being impressed with the software development kits for the console.

The game was originally a completely original IP during its early development stage. However, Itagaki was asked to title the game Ninja Gaiden so the game could be easily marketed to foreign markets.

The German rating board deemed the game's gore and violence excessive and refused to rate the game at all. Since this had the potential to place the game on Germany's "List of Media Harmful to Young People", banning shops from either advertising or selling the game to customers of 18 years or older, Tecmo censored the PAL version to obtain a rating. A year later, Tecmo managed to obtain an 18+ rating for the uncensored release of Ninja Gaiden Black.

In the DLC update, Ninja Gaiden Black, Ayane's kunai messages featured fully voiced dialogue, which was not a feature in the original version. In Ninja Gaiden Sigma, the text and dialogue that explained the controls were changed to reference both PlayStation 3 controls and altered mechanics.

In the first level of Ninja Gaiden Black, if the player dies 3 times, the game will ask if they wish to "abandon the way of the Ninja?" After double verifying "Yes", a scene of Ayane coming to Ryu's collapsed body will play, unlocking Ninja Dog Mode, an easier difficulty setting. From then on she will provide additional messages throughout the game that won't be seen in a regular playthrough, with healing items and artifacts that make the game easier. Once per chapter, if the player (or an allied NPC) dies in this mode, the game will provide additional healing items. In addition, all Results scores will say "Ninja Dog", and the title screen will feature an image of Ayane instead of Ryu.