About 145 pilot whales have died following a mass stranding at Mason Bay on Stewart Island.

A Department of Conservation (DOC) spokeswoman said a tramper found the whales on Saturday and notified DOC staff at 10.30pm.

The two pods had stranded at the southern end of Mason Bay, about 2 kilometres apart.

DOC Up to 145 pilot whales have stranded and died on a remote beach on Rakiura/Stewart Island over the weekend.

DOC Rakiura operations manager Ren Leppens said half of the whales had already died and the decision was made to euthanise the rest due to the condition they were in and the remote location where they were stranded.

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"Sadly, the likelihood of being able to successfully refloat the remaining whales was extremely low. The remote location, lack of nearby personnel and the whales' deteriorating condition meant the most humane thing to do was to euthanise.

"It's always a heart-breaking decision to make."

Project Jonah general manager Daren​ Grover​ said pilot whales are not endangered, but their total population is unclear so it is hard to say what the long-term toll of a large stranding could be.

The southern hemisphere long-finned pilot whale lives throughout the Southern Ocean, but the size of the population is not well understood, DOC's website says.

Marine mammal strandings are a relatively common occurrence on New Zealand shores, with DOC responding to an average 85 incidents a year – mostly of single animals.

Several stranding happened across New Zealand over the weekend. On Sunday, 10 pygmy killer whales stranded at 90 Mile Beach and a sperm whale beached in Northland. A dead female pygmy sperm whale also washed up at Ohiwa over the weekend.

Grover said there was usually at least one "significant" mass stranding a year. Stewart Island was a common spot for whales to become stuck.

More than 650 pilot whales beached themselves along Farewell Spit at top of South Island in two separate mass strandings last year, the largest of its kind in New Zealand for almost a century. The biggest recorded pilot whale stranding was an estimated 1000 whales at the Chatham Islands in 1918.

The 19km stretch of beach at Mason Bay could be "confusing" for whales, he said. Whales use echolocation signals to communicate, but gently shelving waters in the area could distort those signals – a possible cause of strandings in the area. It would also explain why most mass strandings happened in summer, when whales followed popular food sources inshore.

Exactly why whales and dolphins strand is not fully known, but factors can include sickness, navigational error, geographical features, a rapidly falling tide, being chased by a predator, or extreme weather. More than one factor may contribute to a stranding.

Whales can only swim forward, so can also become stuck as the tide recedes.

"It could be that they are swimming forward, then the tide changes and they're unable to turn around because they can't swim backwards so there really is no place to go."

Stewart Island's population is extremely low, even in the peak of summer, meaning there are "very few people to keep an eye on the shore". Grover said stranded whales needed to be tended to quickly because of predator and seagull attacks, dehydration, and the onset of heat exhaustion.

DOC has notified Ngāi Tahu of the Mason Bay stranding and is working with the iwi on what to do next.

Southland District councillor Bruce Ford said it was not unusual for pilot whales to strand at Mason Bay.

"It happens sometimes ... in days of old they would have harvested them [for whale oil]."

In 2011, a pod of 107 pilot whales was found beached at Mason Bay by two tourists.

The pair – who had tramped to Mason Bay hut, on the west coast of the island – found the pod dead and dying at the southern end of the beach near Cavalier Creek.