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.