The Department of Conservation confirmed a tourism operator made the sad discovery at Scenery Nook near Christchurch.
Seals are protected by New Zealand law. The dead pups were estimated to be 11 months old.
“Due to the disturbing, brutal and violent nature of this crime, it has been reported to the police,” said the Department of Conservation operations manager Andy Thompson.
“We believe it’s incredibly unlikely sharks would have bitten the heads off six seals but left the bodies untouched.
“Regrettably, antagonism towards seals is often due to the misplaced belief that seals are eating large amounts of fish species valued for human consumption.
“That isn’t the case. Research shows 90 percent of Banks Peninsula fur seal diet is made up of lantern fish which are not sought after in fishing.”
In 2011, a New Zealand teenager was jailed after killing more than two dozen seals.