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.
Although Ninjemys was initially categorized under the genus Meiolania, Gaffney argued in 1992 that it is morphologically distinct from the genus. Placing Ninjemys within Meiolania would either make the genus paraphyletic or necessitate changes to its diagnostic characters, leading Gaffney to create the genus Ninjemys to maintain the original classification of the genus. Additionally, a thorough examination of Ninjemys revealed that in some respects it was more akin to the older Niolamia from the Eocene of Argentina.