The discovery of two Hector's dolphins washed up at beaches in the South Island is raising fresh questions over whether enough is being done to protect the endangered species.

Photo: 123RF

The Ministry for Primary Industries said it was investigating the deaths and there were indications both dolphins could have been "subject to human interference".

A member of the public found one dolphin on a Greymouth beach last month, while the second dolphin was found near Banks Peninsula on Sunday.

MPI compliance investigations manager Gary Orr said the deaths were very concerning.

"MPI and [the Department of Conservation] are investigating the circumstances surrounding both mortalities.

"Our investigation will look to identify everyone who was fishing in the areas prior to the discovery of the dolphins.

"MPI is working closely with our colleagues at DOC to ensure we get to the bottom of this and to hold to account, the person or people responsible."

The people who found the dolphins did the right thing by reporting them, Mr Orr said.

"We encourage anyone in a similar situation to do the same. Any dolphin death is one too many."

Under the Marine Mammals Protection Act, anyone who kills or injures a marine mammal must report the event. Neither death was reported to authorities.

A marine aerial survey conducted last year estimated the Hector's dolphin population at between 12,000 and 18,500 - twice as many as previously thought.

However, the species is still listed as endangered and there are restrictions on commercial and recreational fishing in the dolphin's known habitat.

Mr Orr said he did not want to compromise the investigation by saying too much about how the dolphins died.

But he said it was rare to find them washed up.

"As with most things that die in the ocean, there are a number of other species that predate on dead mammals so it's particularly important that when they do wash ashore that they are reported to us so we can learn from why it died."

MPI was interviewing everyone known to have been fishing in the area at the time the mammals were thought to have died.

Dispute over dolphin numbers

While only two of the dolphins had been reported as being killed by commercial fishers in the past year, it was thought the true number could be as high as 77.

"That's always a concern that there is under-reporting and the ministry is taking steps to implement monitoring programmes, particularly for commercial vessels that may help us identify mortalities in the future," Mr Orr said.

The ministry estimated there were about 15,000 Hector's dolphins.

But Otago University dolphin expert professor Elizabeth Slooten said this figure was misleading and on the West Coast, where one of the dead mammals was found, the population had fallen 20 percent in the past 16 years.

"We have done an analysis on how many dolphins are being caught and what we expect to happen with these separate populations and we predicted it would drop by 1000 but not until 2050 ... And so that drop has occurred but much much faster than we predicted."

MPI was also underestimating how many Hector's dolphins died in nets each year, she said.

She cited a NIWA study showing up to 150 died this way each year, nearly double MPI's figure.

"That's the problem at the moment is that there's very very poor information, even on the number of dolphins caught in gillnets and the number of dolphins caught in trawl nets, basically all we have is a 'yes' answer.

"We know that they get caught in trawl nets but there's been so little observer coverage on trawlers that there is no way of estimating how many."

Pods of up to 60 Hector's dolphins at a time had been seen following trawl nets in New Zealand waters, attracted by the prospect of an easy meal.

"So it really is, you know, like a child playing in the traffic. There's been some very good research done on this in Australia with bottlenose dolphins where they put cameras in the nets, and I have some footage of bottlenose dolphins swimming in and out of trawl nets and spending quite some time in those nets. So fish that have been caught, they pick them out."

MPI believed the chances of finding out who killed the two dolphins were low, but said it was important to establish how they died to prevent it from happening in future.