The search has been halted due to darkness and weather constraints but it will resume at first light today with a helicopter scanning the waters.
"Anything could happen, whales could change direction, flight going up in the morning to locate whales again," an official National Oceanic and Atmospheric Administration account tweeted.
The agency is coordinating the search.
With 11 whales already dead, a second NOAA tweet said biologists were concerned to hear of behaviour including dehydration and malnutrition among whales being monitored.
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We are "hoping they are out to sea," Mase told reporters in a conference call.
The mysterious mass stranding in a remote area off the US state's Everglades National Park was first reported on Tuesday. Some of the whales are unaccounted for amid fears they died and sank to the ocean floor.
Of the 11 that perished, four had to be euthanized after they became unable to breathe, hydrate and feed in the shallow waters less than three feet deep off Highland Beach on the Gulf Coast.
Of the remaining whales that have been sighted, seven were in dangerously shallow waters of 12 to 14 feet, about five miles offshore and southwest of where they were originally stranded, Mase said.
Another two were "swimming freely" around Plover Key, she said, adding that a biologist was on his way to the area to assess their condition.
While a preliminary NOAA assessment put the total number of stranded whales at 51, officials yesterday said they did not have an exact figure.
But with the clock ticking, NOAA has stressed that the rescuers were treading cautiously as sharks have been seen feeding on the dead whales' carcasses.