The two children, aged one and two, were discovered unresponsive by officers in Queensland on Saturday. It is not clear how long they had been inside the car.
The two girls showed evidence of being exposed to extreme heat, a police officer stated.
Temperatures at the time they were found in the vehicle, in a town close to Brisbane, were about 31C (88F).
Their mother, Kerri-Ann Conley, 27, is the first person set to be charged with murder after Queensland state broadened the definition of murder to include “reckless indifference to human life”.
She has been also charged with possessing drugs and utensils or a pipe, according to an ABC report.
Queensland State Premier Annastacia Palaszczuk referred to the children’s’ deaths as “an absolute tragedy” and stated the Department of Child Safety would look into the case.
“I was heartbroken when I heard about it,” she added.
She also said the children were known to the Department of Child Safety.
Queensland police were called to the vehicle together with paramedics, who tried to revive the children, and both were declared dead at the scene.
Tributes to the children have been left outside their residence in Logan, south of Brisbane.
Detective Mark White says a witness has come forward and is assisting police with their probe.