Scientists have discovered there are more Hector's Dolphins in New Zealand than the previous population estimate.

A team from Nelson's Cawthron Institute have discovered there are potentially twice the number of Hector's dolphins in New Zealand waters than previously realised.

The findings of a three-year marine aerial survey to update the dolphin's population and distribution show there are between 12,000 and 18,500 dolphins, almost double the last estimation of 7000.

Hector's dolphins are one of the world's rarest dolphins and at only 1.4 metres long and 50 kilograms they're also one of the smallest. The species is listed as endangered.

Martin de Ruyter Cawthron Institute scientist Deanna Clement led the three-year survey to update the Hector's Dolphin population and distribution.

Cawthron Institute marine mammal ecologist Dr Deanna Clement who led the project said it was exciting that the findings were so positive.

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"It is not often that you find something new about a species that has been studied so thoroughly for so long."

The survey was done by plane with the dolphins counted and measured from the air while previous surveys had been done by boat.

Hector's dolphins were previously thought to be a mainly inshore species, however Clement's team found up to half the population in unprotected waters beyond four nautical miles offshore.

Clement said while the numbers were reassuring, it didn't mean the species were no longer at risk.

Set nets and trawl fishing were the biggest threats to dolphins in New Zealand, those fishing practices have been banned in New Zealand up to four nautical miles offshore around most of the South Island to protect them.

"While there had been unconfirmed sightings as far out as 15 to 16 nautical miles offshore, up till now it had been difficult to accurately survey that far out to sea in New Zealand," Clement said.

It was the most intensive marine aerial survey ever conducted in New Zealand.

More than 670 hours were spent surveying from the air, up to 20 nautical miles offshore, covering an area of 75,196 square kilometres. The areas were surveyed twice, during summer and winter, which totalled an area the size of the South Island.

They were found throughout the South Island waters. Research confirmed a small population exist in the Golden Bay area with a larger population in Queen Charlotte Sound.

Clement said while they weren't often seen near Nelson, a small group were observed off the Boulder Bank last summer.

New mathematical and survey methods developed during the research allowed for more accurate data to be collected and have since been endorsed by the International Whaling Commission (IWC).

"We have made some evolutionary steps forward, so it is kind of nice, little New Zealand working on their little dolphin, now these can go out and be applied to a lot of other countries and a lot of other species."

Clement said policy makers had been provided with with robust scientific evidence so they could make effective decisions around protecting and managing Hector's dolphins.

The project involved a multi-disciplinary team of scientists, PhD students, pilots and Government agencies - the Ministry for Primary Industries and the Department of Conservation.

Primary Industries Minister Nathan Guy said the survey had been independently peer-reviewed and endorsed by scientists at the International Whaling Commission which gave an assurance the numbers were scientifically robust.

"The results of the survey will be one consideration in the ongoing risk assessment for the species, and will factor into the Hector's and Maui's dolphin threat management plan which is due for full review in 2018," Guy said.

The Hector's and Maui dolphin threat management plan has been in place since 2008, it identifies human-induced threats to the populations and outlines strategies to mitigate those threats.