Doctors typically wear protective gloves and cover the probe with a condom.
In most cases, the probes are cleaned with liquid disinfectant.
Dr McNally, the past president of the Australasian Society of Ultrasound in Medicine, presented the results of his study at an international conference in Sydney on Wednesday.
He says the study helps doctors appreciate that handles are a potential source of infection.
"It is not just the tip of the probe that we should be concerned about."
The study was sponsored by Nanosonics, an Australian company that makes a device designed to disinfect the entire probe.