With the loss of their powers, Zordon sent the Rangers to find the maker of all the Power Coins, the mysterious Ninjor. After proving themselves, Ninjor created six new Coins which drew on the power of six animal spirits that represented each Ranger (the Red Ape, the Pink Crane, the Blue Wolf, the Yellow Bear, the Black Frog, and the White Falcon). With their new Coins and powers, the Rangers received the true power of the Ninja along with new Ninjazords. Despite this complete change in Power Coins, they retained their dinosaur and white tiger motifs on their suits, suggesting that the new Ninja Power Coins simply restored the Rangers connection to the Morphin Grid through a new link and activation "Call" while enhancing them with the ninja powers.

Unlike the Dinosaur Coins, the Ninja Coins drew on the life force of each respective Ranger. This proved to be dangerous when Rita and Zedd were successful in stealing Kimberly's Crane Power Coin thanks to the help of their brainwashed pawn Katherine Hillard, but the Power Coin is later returned to Kimberly. When Kimberly decided to retire, she gave her coin to a now-reformed Katherine.

When Master Vile used the Orb of Doom to reverse time on Earth, the Rangers become powerless kids; the reason they could no longer morph was because at the age they had been reverted to, they had not received their powers. Though as a bright side, the Ninja Coins allowed the Rangers to maintain their true memories. With help from Billy, Cestro created a regenerator using the Ninja Coins as a power source. However, only Billy returned to his true age before the device was destroyed by Rito and Goldar. Goldar and Rito teleported into town and chased after the kids. They managed to steal their Coins and bring them to Zedd and Rita. With the two firing blasts from their staffs, the Ninja Coins were destroyed and reduced to dust in Goldar's hands.

Several years later following the creation of the Master Morpher. Tommy's White Falcon Ninja Coin was recreated within the White Tiger Power Coin and placed within the Morpher before the battle with Lord Draven.