Most of the 39 pilot whales stranded in Golden Bay on New Zealand’s South Island will be put down because it is almost impossible to refloat them.

The large whales – some up to 5m long – stranded themselves on Sunday night on a high tide at the base of Farewell Spit in the first mass stranding in the area this summer.

NZ Department of Conservation staff had been monitoring the pod since Sunday lunchtime, but because of high winds were unable to ward them off the beach, DOC Golden Bay area manager John Mason told AAP.

Staff returned on Monday morning to find the 39 had stranded themselves at the top of the high tide mark, which was followed by a lower than normal tide.

Twelve of the 39 had already died and the remainder would be shot, Mr Mason said.

It would have been impossible to rescue the whales, he said.

“The fact they were so far up the beach and so big, and with the tide, we just don’t believe we can get them off the beach and out to sea.”

Pilot whales are regular mass stranders on New Zealand shores, especially in the peak stranding season from November through to March.

Strandings are common on the 24-kilometre long Farewell Spit at the top of the South Island and whales often beach themselves again after being refloated.