Several horses have already been listed on the Lost Horse register.
The toll of horses is unknown, as the cleanup across the state gets under way.
To date, 80 standardbreds are known to have perished at Cold Mountain Stud, but the equine death toll is certain to go much higher.
Sixteen people are confirmed dead in the flood, with the death toll predicted to double in the next couple of days. About 50 people are still missing.
The council said it was working with an online connection through Pet Reconnect, which has started the list of missing and found horses.
The service also includes domestic pets.
The Queensland Horse Counsil said: "As many identifying features are required, even on dead animals. We want to be able to bring some closure to owners who have lost horses and also have accurate figures of lost horses at the end of this."
The Pet Reconnect page makes sad reading.
Word is wanted on Nardia, a fleabitten grey Arabian mare, whose former owner wants word on her fate from her new home at Caboolture.
Another owner lost a brown yearling colt and two-year-old bay gelding in water in Helidon Spa. Ellie says: "They will surely be deceased but I would like to find them if possible."
Word is also wanted on a black Shetland pony missing from Waters Road Calvert, outside Rosewood, during the flood on Tuesday.
"This pony belongs to my daughter. She is a 'mini trotter' and is irreplaceable," said Kim.
A brown yearling colt was reported to have gone down into Neurum Creek from a Mount Delaney property.
However, not all the news is bad.
"Help needed," reported one person. "Rescued four donkeys yesterday on Beachmere Rd and some[one]else got [a] foal yesterday.
"We need the foal with its mum, please."