Police have been called in after six fur seal pups were found decapitated in a popular Christchurch bay.

The 11-month-old seals were discovered by a tourism operator floating in the tidal wash at Scenery Nook on the south side of Banks Peninsula on Monday.

When the Department of Conservation visited the bay, they couldn't find the seals' heads and believe they may have been killed elsewhere before being potentially dumped from a boat and left to be found by visitors to the scenic bay.

DoC Mahaanui operations manager Andy Thompson called the deaths "cruel and senseless".

"Due to the disturbing, brutal and violent nature of this crime against defenceless seal pups, it has been reported to the police," he said.

Fur seals/kekeno are protected under the Marine Mammals Protection Act and it is a criminal offence to harass, disturb or harm them.

Three of the seals have since been buried by DoC rangers, the other three have been sent to Massey University for a necropsy.

"While the necropsy will determine the exact cause of death, we believe it's incredibly unlikely sharks would have bitten the heads off six seals but left the bodies untouched," Thompson said.

DoC is appealing for any sightings of boats in the area since late last week.

"There were a lot of boats on the water enjoying the warm weather last weekend. If you saw anything suspicious, please let us know by ringing 0800 HOT DOC (0800 362 468)," he said.

There are several known cases of people injuring or killing seals after becoming frustrated over low fish numbers in the ocean.

"Regrettably, antagonism towards seals is often due to the misplaced belief that seals are eating large amounts of fish species valued for human consumption," Thompson said.

"That isn't the case. Research shows 90 per cent of Banks Peninsula fur seal diet is made up of lantern fish which are not sought after in fishing.

"If people wish to ensure healthy fish and shellfish populations around Banks Peninsula, they should ensure they respect catch sizes and limits and make it their business to report illegal fishing in the peninsula's marine reserves.

"Last weekend, DoC's marine rangers interviewed eight people who appeared to be fishing illegally in the Pohatu Marine Reserve near Akaroa."

Last year 16 people were prosecuted for fishing in the Banks Peninsula's two marine reserves, Pohatu and Akaroa, which together make up less than 2 per cent of the peninsula's ocean. Under the Marine Reserve Act it is illegal to take anything from a marine reserve.

"I can't believe people are willing to run the risk of a life-long criminal conviction over a couple of fish. People need to understand these reserves are protected and they will be charged if they are caught fishing here," Thompson said.

Monitoring shows the fish life inside the two reserves is more abundant than other parts of the Banks Peninsula and this has flow-on benefits for ocean life outside the reserves.

The reserves can be used for recreational activities such as snorkelling and kayaking, however it's a strictly no take policy.