The University of Otago Animals, Aquatic, Plants and Ecological Society (AAPES) was on a group trip to the Catlins last week when it discovered the pup suckling from its mother at Purakaunui Bay.
Group vice-president Taylor Davies-Colley said the group was surprised to see a mother suckling a pup, as they knew how rare pups were on the mainland.
''Everyone was excited to see it,'' he said.
Doc Coastal Otago biodiversity ranger Jim Fyfe said the pup was born on Dundas Island last year. It was tagged by Doc in January this year.
This was the first known record of a mother sea lion bringing a pup more than 500km to mainland New Zealand from the Auckland Islands.
Young male sea lions had been known to travel from the Auckland Islands on their own once they were weaned, but it was unusual for a pup to travel to the mainland with its parent.
''This particular migration is very special.''
Most sea lion mothers utilised ''tried and true foraging areas'' and kept their pups safe within swimming distance, Mr Fyfe said.
''For this mother to choose to migrate and bring her pup is something quite extraordinary.''
Female sea lions also rarely travelled between the islands as they typically bred where they were born.
''Hence just a few adventurous ones arrive.''
He warned people to stay at least 10m from sleeping sea lions, vehicles should remain at least 50m away.
The low genetic diversity and a declining overall population meant each individual sea lion was ''extremely important'' and sightings were of great interest to Doc and the New Zealand Sea Lion Trust.
Mr Davies-Colley said finding out where the pup came from only ''made the experience that much more special'' as it could mean further repopulation of the species on the mainland.
The New Zealand sea lion is the rarest in the world and is classified as nationally critical.
The number of sea lion pups born in the Auckland Islands dropped from 3000 to 1500 pups between 1998 and 2009.
