Ninjutsu is very powerful ninja magic that could be used to kill or defeat enemies. They were used by collecting magic scrolls called Makimono. There were many types of ninjutsu:
Shinobi III: Return of the Ninja MasterEdit
- Jutsu of Ikazuchi - Pull down a lightning bolt to make Joe temporarily invincible.
- Jutsu of Kariu - Summon the flame of Kariu - four devestating pillars of fire that becomes a whirlwind of destruction to any enemies on-screen. 
- Jutsu of Fushin - Mysterious ghost images of Joe Musashi appear, multiplying his jumping ability. 
- Jutsu of Mijin - This Jutsu destroys enemies by causing Shinobi's body to become a living bomb. (Be warned, Shinobi looses one life per use of Mijin.) 
Shinobi (2002) Edit
- Ka'en - Unleashes a flame burst, killing or harming all enemies within the radius. Hotsuma can use this once per Makimono .
- Kamaithachi - Using Hotsuma's sword, hurl shock waves at his enemies. This can used once per Makimono.
- Raijin - This magic makes Hotsuma invincible from attack or damage from enemies for a short peroid of time. This can used only a certain amount of times per Makimono.
: Shinobi III: Return of the Ninja Master Sega Genesis Guide