Although Ninjemys was initially placed in the genus Meiolania, Gaffney argued in 1992 that it is morphologically distinct from the genus. Continuing to place Ninjemys in Meiolania would either render the genus paraphyletic or require the diagnostic characters of Meiolania to be altered, with Gaffney creating the genus Ninjemys to retain the prior diagnosis of the genus. Furthermore, detailed study of Ninjemys showed that in certain regards it was more similar to the much older Niolamia from the Eocene of Argentina.
Gaffney argued in 1992 that Ninjemys should not be placed with Meiolania due to its distinct morphology. If classified within Meiolania, this could make the genus paraphyletic or require changes to its diagnostic features. To maintain the original classification, Gaffney introduced the genus Ninjemys. Further study revealed that Ninjemys was more similar to Niolamia from Argentina's Eocene period.