It took two tractors and another digger to dislodge the digger as it had sunken well into the sand by that stage.
Mr Whalley said the digger was a write-off and a replacement, without the same level of attachments as on the lost digger, would cost more than $100,000.
And while he was insured, he said he would still be left seriously out of pocket.
Northland Regional Council said Wal's Holes did everything right by informing it straight away that there was a potential environmental hazard in the marine environment.
NRC spokesman Colin Dall said the council was concerned about any possible fuel leaks into the harbour, but there were no significant adverse affects caused by the digger being in the tide overnight.