"Human interference" could be involved two separate Hector's dolphin deaths in different parts of the country, the Ministry for Primary Industries says.
The ministry and the Department of Conservation have launched an investigation into the deaths of the endangered species in Greymouth last month and near Banks Peninsula on Sunday.
Both were found by members of the public.
MPI Compliance Investigations Manager Gary Orr considers the deaths "very concerning" and there's some suggestions humans may have had a hand in it.
The Marine Mammals Protection Act requires deaths and injuries to be reported to authorities, but that was not done in either case.
"Our investigation will look to identify everyone who was fishing in the areas prior to the discovery of the dolphins," Mr Orr says.
The penalty for commercial fishers is a fine of up to $100,000, while a recreation fisher faces a $10,000 maximum fine.
He praised the members of the public who did report the deaths and encouraged others to do the same should they come across a similar grisly discovery.
The Hector's dolphin is one of the smallest dolphins in the world, measuring no longer than 1.5m and are only found in New Zealand.
They're normally found around the coast of the South Island, with populations concentrated between Haast and Farewell Spit, Banks Peninsula and Te Waewae Bay and Porpoise Bay/Te Whanaga Aihe.
There are thought to be fewer than 8000 of the animals left in the wild, down from around 29,000 in the 1970s.
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