Repatriation Hospital at Daw Park in Adelaide has been reported to have critical leaking roofs and animal droppings which poses health risks to its patients, says The Australian Medical Association (AMA).
It says leaks are putting chronically-ill people at risk of getting pneumonia or other illnesses.
The AMA says some patients have to be dried off by staff before they can go into surgery.
AMA president Andrew Lavender says corridors near the operating theatres are affected by leaks.
He says animal faeces from the roof can also get into the hospital when it rains.
With water flowing from a roof with potentially rodent or possum poo in there, I think we've actually got a great risk, particularly in people who are ill or have other chronic illnesses of developing unusual types of pneumonias and becoming very, very sick from that, he said.