UPDATED 1.13PM Volunteers have refloated the remaining 17 whales that became stranded in Golden Bay last night.

LISTEN ABOVE: Marine biologist Dr Rochelle Constantine speaks to Andrew Dickens

Most of the second pod of 240 stranded whales had managed to re-float themselves overnight.

Only 17 remained beached this morning, eight kilometres down the bay from where 417 whales stranded on Thursday.

The whales are headed in the direction of a large pod milling in Golden Bay but authorities are concerned they may turn back in, the Department of Conservation's Herb Christophers says.

"We have boats on the water trying to manage their egress from the sandy shore," he said.

"It is looking hopeful, but they may yet come back in so we are trying to avoid that.

The original stranded pod wasn't so lucky, only 80 were re-floated and around 300 died prompting questions as to how the pilot whales became stranded in the first place.

Callers into Newstalk ZB believe earthquakes may be confusing the animals and there have been instances in the past that suggest there could be links.

More than a hundred beached at Stewart Island just before the Christchurch 2011 earthquake, fast forward to this week and the now more than 600 that have beached in Golden Bay's Farewell Spit.

It was shortly followed by this morning's 5.2 magnitude quake near Culverden.

But Auckland University Marine Biologist Dr Rochelle Constantine told Andrew Dickens Farewell Spit is a natural trap for whales and she's not convinced there's a link.

"They may well be able to sense the earthquakes but these animals live with these sort of geological natural phenomena all the time in New Zealand and yet we don't get a stranding every time there's an earthquake."

Local iwi representatives have provided a karakia, or prayer, over the dead whales.

This week's event is the third-largest recorded stranding in New Zealand since data started being collected in the 1800s.

About 1000 whales beached themselves on the Chatham Islands in 1918 and 450 in Auckland in 1985.