Scientists are this week heading to the subantarctic Auckland Islands for an annual survey of white-capped albatross and New Zealand sea lion numbers in the remote and windswept region.

White-capped albatross are endemic to New Zealand and breed on the Auckland Islands in the Southern Ocean, 465km south of Bluff.

The survey, carried out by helicopter, will track albatross population size and trends.

Hundreds of thousands of the white-capped albatross breed on the Auckland Islands each year, estimated to be over 95 per cent of the worldwide population.

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In its ninth year, this year's white-capped albatross census is a collaboration between the Department of Conservation, Seafood New Zealand, Deepwater Group and the Ministry for Primary Industries.

Funding in previous years had come from either DoC or MPI, but because of limited resources due to Conservation Services Programme efforts on the Chatham Islands, others were needed to step up.

"The survey allows us to create valuable datasets that give consistent information on breeding patterns and adult populations," said Richard Wells of Deepwater Group, a co-operative of deepwater fisheries quota owners.

A survey of New Zealand sea lion pups will take place simultaneously.

The New Zealand sea lion is the world's rarest sea lion and classified as nationally critical, and around two thirds of all pups are born at the Auckland Islands.

The sea lion survey has been running since 1996 and will focus on three different locations: Sandy Bay on Enderby Island, Dundas Island and Figure of Eight Island.

The 2016 survey estimated there were 1727 pups on the island, a 15 per cent increase on the lowest estimate from 2009.

The sea lion census is funded by the Department of Conservation.