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The whale was spotted on the beach on Saturday by a Glacier Country Helicopters pilot, who reported the sighting to the Department of Conservation.
Doc staff discovered the jaw had been removed on Sunday morning when visiting the site with a Te Runanga o Makaawhio representative to establish a possible cause of death, gather scientific data and assess the whale for suitability for cultural or scientific recovery. There was no obvious cause of death.
Makaawhio chairman Tim Rochford said iwi and Doc had well-established protocols around the treatment of whale bone which were in place to protect the mana of the whale.
''It is extremely disappointing that someone would disrespect these protocols and our taonga.''
Doc works with iwi and whale experts to recover cultural materials from whales which are used by iwi for ceremonial purposes. It is illegal to take whale bone without a permit.
Doc senior ranger Guinevere Coleman said the whale had likely been dead a couple of weeks before it washed up.
''As well as being illegal and insensitive, cutting into a whale carries significant risks - whales carry disease and bacteria that can be very dangerous for people.
''We encourage anybody who has information about the jawbone removal to contact the Franz Josef Doc office or the Doc hotline (0800 DOCHOT). The jaw is likely to be well over 1m long and difficult to remove from the site. A boat and quad bike or a helicopter would have been required to move the jaw.''
The unauthorised removal of whale bone contravenes the Marine Mammals Protection Act 1978 and can result in imprisonment for up to two years or a fine of up to $250,000.