The Scottish SPCA is now investigating and said the animals were killed in a way which have caused a “great deal of suffering”.
One female had been shot with her head removed and taken away. She had also been cut open, exposing her dead young.
The other female had a broken neck and a shot wound to the head.
They were discovered at the car park on Golf Road in Ellon, Aberdeenshire, on 7 May.
The animal welfare charity suspects the deer were killed in a poaching-related incident and is appealing for information.
Scottish SPCA Inspector Fiona McKenzie said: “The black bags contained the remains of two pregnant adult females and a fawn.
“They had been illegally killed in a way that would have caused a great deal of suffering.
“A post-mortem of the deer showed that one of them had a broken neck and a shot wound to the head, however we’re unsure which would have caused her death.
“The other female had been shot and had her head removed, which was not present amongst the remains.
“Her uterus had also been cut open, exposing her dead young.
“We suspect the deer were killed in a poaching-related incident and although deer can be killed lawfully, it is closed season which is given to female deer to protect their welfare and that of their young. Closed season takes place from 1 April to 31 October.
“We are urging members of the public with information about this incident to contact us as soon as possible. Calls are treated in the strictest confidence and can be left anonymously.”
Details of the fawn’s injuries were not available.
Anyone with information is being urged to contact the Scottish SPCA animal helpline on 03000 999 999.
Last year police wildlife crime officers carried out anti-deer poaching patrols in the Highlands and Islands.
Operation Moon was launched to target known poaching “hotspots”.
Officers at the time said poachers are also often involved in other rural crimes and urged residents to get in touch with any information regarding rural crime.