The Black Ninjas are the enemies of the White Ninjas and are allied with the KGB. They are the "bad guys" of the ninjas, given by how they attack civilians, cops, and the army.
They guard Dr. Go! in Castle Kuro alongside the KGB when the latter kidnapped him, who was then rescued by Crypto, as he has knowledge of the hidden KGB base.
Crypto later retrieves one of the three codes needed to access the base from Dr. Go's stolen briefcase from the Black Ninjas' base. The player can do this either by disguising himself as one of them and tricking their leader into handing it over, or the hard way by attacking their base head on, killing all of the ninjas guarding it, and taking the case.
In the Arkvoodle cult missions, Crypto convinces them to worship Arkvoodle after telling them that Arkvoodle is better than the evil God "Darkvoodle". They instead plan to sacrifice him, but Crypto defeats all of the ninjas before they reach him. The Black Ninjas later join all of the factions, the cops, army, KGB, and Yakuza, in attacking the cults' tents, still bitter about Crypto tricking them about "Darkvoodle." Crypto fends all of them off.