A tip-off on Saturday led police to a truck parking bay near Glen Innes in northern New South Wales state where they made the grisly discovery.
Police said they were baffled.
"An initial examination of the animals did not reveal any obvious wounds or indicate a cause of death," they said in a statement.
"There were no brands, tags or any other form of identifying marks that could be seen to assist the officers in locating an owner."
The 25 ponies, of various colours and ages, were in the early stages of decomposition.
Officers photographed the animals then buried their remains at the site, appealing for anyone who witnessed any suspicious behaviour to come forward.