The controls of "Shinobi" consist of an eight-way joystick and three action buttons for attacking, jumping and using ninjutsu techniques (also called "ninja magic" in the game). In addition to the standard walk, the player can perform a crouching walk by pressing the joystick diagonally downward. The player can jump to higher or lower floors by pressing the jump button while holding the joystick up or down. The protagonist Joe Musashi's standard weapons are an unlimited supply of shurikens, along with punches and kicks when attacking at close range. Rescuing certain hostages in each stage will grant him an attack upgrade. When powered up, his throwing stars are replaced by a gun that fires large, explosive bullets, and his close-range attack becomes a katana slash. Musashi's ninjutsu techniques can only be used once per stage and will clear the screen of all enemies, or in the case of enemy bosses, greatly damage them. There are three ninjutsu techniques in the game (a thunderstorm, a tornado and a doppelganger attack) that vary depending on the stage, although the effect is the same no matter which technique Musashi uses (only the animation changes).