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The bodies of six fur seal pups have been found decapitated in a popular bay on New Zealand's South Island.

The 11-month-old seals were discovered on Monday by a tourism operator in Scenery Nook in Christchurch, said the Department of Conservation (DOC).

The seals' heads could not be found and the DOC believe the seals were killed elsewhere before being dumped from a boat.

It has called the incident "cruel and senseless".

said DOC Mahaanui Operations Manager Andy Thompson in a statement.

He said the DOC had ruled out a shark attack, saying it was "incredibly unlikely sharks would have bitten the heads off seals but left the bodies untouched."

Three seals have been buried by DOC rangers and the other three bodies will be taken to Massey University for examination. The DOC has appealed for any witnesses to come forward.

It is a crime to harass, disturb or harm fur seals under New Zealand's Marine Mammals Protection Act.

Mr Thompson said there have been cases before of people injuring or killing seals after becoming frustrated over low fish numbers.