A statement from NCI said the machine, named Gadi (meaning "search for") would also have its own artwork designed by renowned Ngunnawal artist Lynnice Letty Church.
The naming has been done in consultation with the United Ngunnawal Elders Council.
The artwork represents the coming together of western and Indigenous knowledge systems, guided by Ngunnawal Elders over many generations, according to Church.
Renowned artist Lynnice Letty Church next to the artwork. Supplied
Said Church: "The art symbolises the gathering of knowledge from different places and sources, and the bringing together of an even greater collective knowledge system."
NCI director Professor Sean Smith said: "We are proud to be able to make this connection between the traditional owners of the Canberra region and its newest tool of scientific discovery.
"It is a great honour for the computational research community to have such a perfectly suited name and artwork as the face of Australia's new supercomputer."
The Gadi supercomputer has been funded with a $70 million Australian Government NCRIS investment and delivered by Fujitsu Australia.