"They are not cooperating," Friar said.
Workers also tried to nudge the whales out to sea earlier in the day with no success.
The short-finned pilot whales typically live in very deep water. Even if rescuers were able to begin nudging the 41 remaining whales out to sea, Mase said they would encounter a series of sandbars and patches of shallow water along the way.
This particular whale species is also known for its close-knit social groups, meaning if one whale gets stuck or stays behind, the others are likely to stay behind or even beach themselves as well.
"It would be very difficult for the whales to navigate out on their own," Mase said.
Federal officials were notified about the whales Tuesday around 4 p.m. Because of the remote location, workers were unable to access the site before dark. They arrived Wednesday morning and discovered 45 whales still alive.
"There were some that were very compromised and in very poor condition," Mase said.
Four were euthanized with sedatives, and more could be put down Thursday if their condition deteriorates, Mase said. She described the remaining whales as swimming and mobile but said scientists don't know how long they have been out of the deep, colder water they are accustomed to and could be impacted by secondary consequences, such as dehydration.
"I don't think we have a lot of time," Mase said.
Necropsies were being done Wednesday on the deceased whales. Scientists will look for disease or other signs to indicate how whales got stuck in the shallow Everglades waters.
As workers tried to coax the animals to deeper water, at least one could be seen a few feet from shore floating upside down with its head bobbing up and down. Three to four more could be seen on the beach bleeding.
Twenty-two pilot whales became stranded in Florida's Avalon State Park in Fort Pierce in 2012. Residents, state and national officials attempted to rescue them, but only five could be saved.
"It's not uncommon," Friar said. "But it's not something that happens a lot."
Mase said NOAA was consulting with experts in different counties with experience in herding whales to see if there were other options, but said she was not optimistic.
"The outlook ultimately does not look good," she said.
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Armario contributed to this report from Miami.