The whale, which was around two months old, belonged to the endangered North Atlantic right whale species, of which there are less than 400 remaining.
Any death in the population is a serious setback to rescuing the animals from extinction, officials say.
“This is a very sad event,” said Blair Mase, a whale expert with the National Oceanic and Atmospheric Administration (NOAA).
“Every mortality that occurs really has a devastating impact on the population as a whole because they are one of our most critically endangered whales in the world,” she said. “Every whale counts.”
The calf is believed to have been the firstborn of a 19-year-old whale that biologists named “Infinity.”
Officials are investigating the circumstances surrounding the death but said that it was clear that a vessel was involved. The whale suffered propeller wounds to the head and back.
Bad weather meant that biologists could not immediately search to see if the calf’s mother had also been injured.
Both whales were last sighted off Amelia Island in northern Florida on 17 January.
The right whale population continues to be under threat as ocean vessels, fishing operations, and disease have ravaged their numbers.
The two-month-old was the second calf to have died since calving season, with another baby whale found dead in November on one of North Carolina’s barrier islands.
Since 2017, the animals have been experiencing what biologists call an “unusual mortality event”. At least 33 dead and 13 seriously injured whales have been found, accounting for more than a tenth of the population.
Federal laws prohibit people from harming the whales, and people on the water are supposed to remain at least 500 yards (460 meters) away from them.
“If you’re in this area, please give these animals space,” said Allison Garrett, a NOAA spokesperson.
“The rule is 500 yards — that’s five football fields. That includes people, boats, drones, paddleboards — everything. That’s the law.”
Conservation groups filed a lawsuit last month against the federal government in an attempt to force it to accelerate action on proposals meant to protect the whales.
Scientists have said collisions with ships are one of the greatest threats to the species, which is considered dangerously close to extinction.
“The clock is running out for right whales, and further delay is unacceptable,” Kristen Monsell, oceans legal director at the Center For Biological Diversity, said in a statement at the time.
Ms Garrett urged people who come upon one of the rare whales to report the sighting to officials at (877) 942-5343 to help track their numbers.
Reporting by the Associated Press
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