About 150 people in the human wall were also attempting to prevent some 100 survivors from Friday's beaching from returning to the shore.
Department of Conservation ranger Mike Ogle told Radio New Zealand the whales could have been frightened into the shallows by a shark.
One whale had been found with bite wounds and great white sharks were known to be in the area off Farewell Spit, he said.
"There's one carcass out there with some shark bites in it - but not a big one, just a small one, but quite fresh bites so yeah, there's something out there."
Volunteers were working to refloat some 100 whales believed to be survivors from Friday's stranding at Farewell Spit in the Golden Bay region at the north-western tip of South Island.
The sun was making it difficult for volunteers to keep the whales cool while they waited for the late morning high tide to get the mammals back into the water.
"We have a bit of a problem today with the hot sun which is not good for the whales. We were lucky yesterday with the cloud," DOC official Andrew Lamason told Fairfax Media.
It would take several hours after the whales were refloated to know if the mission had been successful.
The area, about 150 kilometres (95 miles) west of the tourist town of Nelson, is notorious for whale stranding and has witnessed at least nine mass beachings in the past decade.
"If you designed something to catch whales then Golden Bay is probably the perfect design," Lamason said.
When the first mass beaching of 416 pilot whales was found on the beach on Friday morning nearly 300 were already dead.
Pilot whales grow up to six metres (20 feet) long and are the most common species of whale in New Zealand waters.
[brid video="112521" player="7247" title="Fresh whale stranding on notorious New Zealand beach"]
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