The bird, believed to have lived during the 10 million years following the extinction of the dinosaurs, was recovered from greensand rocks near Waipara in 2015 by two fossil collectors Leigh Love and Al Mannering.
The museum's senior curator of natural history, Paul Scofield, said the skeleton, called 'Rosie's Penguin', only just misses out on the record of being the world's oldest penguin fossil.
Rosie's Penguin consists of an almost complete skeleton, missing only its feet and a few other remains.
The oldest, the 62-million-year-old Mannering's Penguin, is also at Canterbury Museum.
Mr Scofield says CT scans and close inspection of the new fossil have found it represents a previously unknown species.
"When Rosie's Penguin was found the consensus among the research team was that it represented a more complete specimen of Mannering's Penguin, which it more or less matched in size and resembled in some skeletal features," he said.
Rosie's Penguin is named after the late wife of the land owner of the farm on which the Waipara Greensand is exposed.