The death of two dolphins at South Island beaches has sparked calls for a nationwide investigation.

The Ministry for Primary Industries said a dolphin was recently found near Banks Peninsula, just weeks after another was found at Greymouth.

Both deaths were reported to the Department of Conservation by members of the public.

It is now investigating whether the dolphins were killed by fishing nets or died of natural causes.

But WWF New Zealand campaigner David Tong says there needs to be a wider investigation, because official statistics don't tell the full story.

"Last year at least one Hector's Dolphin was caught in a fishing net and died on video tape - even though the ministry had the video there was no record of that death on the official statistics."

Mr Tong is concerned they might have been picked up by a set net or conventional trawler.

"If these were killed through fishing then we are be concerned but there may be a systematic issue here - these could be the tip of an iceberg."

The Ministry for Primary Industries previously described the twin deaths are very concerning, as the dolphins may have been subject to human interference.

Under the Marine Mammals Protection Act, anyone who kills or injures a marine mammal must report it.

"MPI and DOC are investigating the circumstances surrounding both mortalities," said compliance investigations manager Gary Orr.

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

He said those who discovered the dead dolphins did the right thing by reporting them to the appropriate authorities.

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

Failing to report a capture attracts fines of up to $100,000 for a commercial fisher and $10,000 for a recreational fisher.

"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," said Orr.