The bones of two whales washed up on a Northland beach have been removed and their remains will be buried.

The marine mammals, believed to be rare pygmy right whales, were found dead on Taupō Bay on Monday morning by locals who notified the Department of Conservation.

A female about 5m long and a calf measuring 2m were about 500m apart with the adult at the mid-point of the bay and the calf at the southern end.

At a meeting between DoC and local iwi, it was decided to flense the whales and to wait for the next high tide between 4pm and 5pm today to wash the mammals away.

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However, environment group He-Manu-Taupunga led by Hori Parata removed the bones, before the high tide.

The group's scientific advisor Jaycee Tipene-Thomas said the bones would be buried at an undisclosed location while the other remains at another location.

She said the bones would be dug up in an year or two and would be kept as taonga.

Earlier today, DoC spokeswoman Abi Monteith said it would be logistically challenging to move the whales.

She said the digger could not do it because the mammals were too heavy and the machine did not have the right parts to carry out the work.

DoC believes the whales are so rare they have only been sighted at sea 30 times.

They are mostly found in Antarctic waters- Taupō Bay was near the northern limit of their range- and they were a pelagic, or migratory, species.