A woman is in Southland Hospital's emergency department being treated for an injury caused by a sea lion pup.

A rescue helicopter evacuated the woman from a remote island about 4.30pm after she was injured by the pup.

The woman, a senior lecturer from the University of Sydney, had been assisting with Department of Conservation research work on Enderby Island, which is part of the Auckland Island archipelago south of Stewart Island.

DoC's senior ranger for the subantarctic region, Jo Hiscock, said the woman was swabbing sea lion pups' mouths when she cut her finger about nine days ago.

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"It was a very, very minor cut - maybe a couple of millimetres wide. It wasn't even a bite, like a chomp, it was just that the seal moved around while she had the swab in its mouth and she didn't move quickly enough with it."

Hiscock said a bite from an adult sea lion was very concerning, but pups were usually less problematic.

"The adult sea lion, they don't brush their teeth, so the bacteria has a while to build up."

The woman's cut did not respond to antibiotics, so the advice of a doctor visiting with a cruise ship was sought.

The doctor recommended she seek hospital treatment.

Hiscock said the woman "looked and sounded chipper" but said she wasn't able to say yet how serious the infection might be.

The Rescue Co-ordination Centre New Zealand (RCCNZ) sent its Southern Lakes BK117 helicopter at 9.40am.

"The 800km round-trip is a delicate operation due to the remoteness of the island," said spokesman John Dickson.

"There are fuel reserves on Enderby Island so the helicopter will refuel before it makes the return journey.

"We expect the helicopter will arrive at the island and to pick up the patient around lunchtime. All going well, they should be back in Invercargill around late afternoon."

Hiscock said the woman was assisting DoC's research into the impact of disease in sea lion pups.