However, a spokesperson for the airline quickly responded to this claim, insisting that the "dog was loaded correctly according to KLM's pet policy."
"The dog's owner has been notified and we express our condolences. In cooperation with the local health authority in the US, the CDC, the dog was initially examined to ensure there was no immediately obvious public health threat," read the statement.
PETA, the animal rights advocates, quickly used the incident to condemn the airline's pet policies as inadequate.
"Tragedies like this one are exactly why airlines must require that animals travel in the main cabin only," read the statement.
The PETA statement urged Air France and KLM to prohibit "companion animals from being flown in the cargo hold, where they endure noise, extreme temperatures and sometimes inadequate pressurisation".
The current Air France-KLM policy allows passengers to keep a dog weighing no more than 7.7kg in the cabin, providing the animal is older than 10 weeks and has all required shots.
Cats and dogs heavier than 8kg must be transported in a container and stored in the cargo hold.
Animals don't receive any food or water during the flight, however, the cargo containers are ventilated.
According to the US Department of Transportation, just over half a million pets were transported in airport cargo holds in 2016.
From those 500,000 animals there were 26 which died, and a further 22 injured. This sets the accident rate at fewer than 1 in 10,000 pets.
However, the causes of these injuries are wide ranging. Changing altitudes, unfamiliar surroundings and the stress of the experience can cause heart or respiratory problems.
The breed of dog can have increased complications on the stress of air travel, in particular snub-nosed breeds such as pugs or bulldogs.
Last year a bulldog died in a 32 degrees C heatwave while waiting to be loaded onto a flight from Townsville Australia.
In the same year a French bulldog suffocated mid-flight on a United Airlines flight, after being loaded into the overhead storage bins.
In 2018 Air New Zealand said it would no longer accept "brachycephalic (snub-nosed) breeds of dogs or cats" on flights with legs more than 5 hours in duration.
Both the owner and the airline are awaiting a full report from the necropsy to provide conclusive insight into the animal's death.