One of three little blue penguins stolen from a burrow recently died during the raid and was left behind.
The capture and removal of the two penguins have raised concerns about the potential smuggling of the little blue birds signalling that this incident at Perfume Point in Napier might not be a one-off.
Department of Conservation (DOC) Hawkes Bay Compliance Officer Rod Hansen said the raid was believed to have happened on 24 January.
A woman was seen with a torch at at 10.30pm as two men used a crowbar to remove three penguins, he said.
The crowbar was used to move the rocks off the penguin's burrow and then hook the birds out around the neck, DOC suspected.
One of the birds died during the late-night raid while the other two were taken away wrapped in towels.
The group then drove off in a white four-door car.
The number of little blue penguins have been declining and are considered an at-risk species.
"We are really concerned as we believe this might not be a one-off," Mr Hansen said.
"The very next day another penguin/kororā was found dead floating nearby and it appears it may have died from a head injury."
He said DOC was not aware where the birds are being taken to and was looking to secure CCTV footage from the surrounding area. He hoped members of the public might have some information.
A number of people were being interviewed about the issue.
"This is particularly disturbing as it is a very vulnerable time for these wee penguins/kororā. They moult from January through to March and stay in their burrows for protection," he said.
"They are nocturnal animals, and the time this offence occurred in the evening, further suggests the poachers knew exactly when best to target the birds."
As the penguins are protected wildlife, the consequences of offences include imprisonment up to two years and a fine of up to $100,000.
Anyone who has any information is being urged to contact the Department on 06 8343111 or 0800DOCHOT.