"We do have some concerns there could be sharks in there, we've put an extra boat in the water.
"One of the carcasses had bites that were consistent with sharks," said DoC area manager Andrew Lamason.
He could not confirm for sure if there were sharks in the water but said DoC was keeping an eye on the situation.
There are also concerns about stingrays in the water and fears the surviving whales could suffer blistering in the hot weather conditions today.
A spokeswoman told the Herald it was not clear yet whether the whales had re-stranded or if they were different whales to the more than 400 which beached yesterday in one of the country's worst ever mass strandings.
Department of Conservation spokesman Herb Christophers said DoC was also uncertain at this stage whether the 100 whales were the same creatures that were refloated yesterday at high tide.
"There are volunteers heading out to care for the whales on the beach, and keep them comfortable," he said.
"A refloat attempt will be made on the high tide around 11.30am."
Whether it was successful or not would be known by 3pm.
Project Jonah asked volunteers to come by 10am, ideally in wetsuits, to help with the refloat at high tide at 11am.
Yesterday 100 whales were refloated at high tide, but 50 returned to the beach and restranded themselves.
Rescuers who tried desperately to refloat the huge pod were due to return at first light today to see how many survived the night.
The Department of Conservation said about 416 pilot whales stranded near the base of Farewell Spit, Golden Bay overnight on Thursday.
Some 250 to 300 were already dead when the whales were discovered early yesterday morning, sparking claims DoC should have acted sooner.
The mass stranding is the third largest recorded in New Zealand since the 1800s.
Volunteers taking part in the mass rescue mission tried to refloat the whales yesterday and kept them cool with damp sheets and buckets of water. Collingwood Area School students also helped out, some singing a waiata to the pod.
Takaka DoC operations manager Andrew Lamason said yesterday the refloated survivors swam in the wrong direction and headed back into the bay.
"There are about 50 [refloated] whales [remaining] offshore, but they're not looking great out there, just milling around," he said last night.
"If you were going to design a geographical trap for whales, Golden Bay is pretty much perfect."