Melbourne Cup runner-up Bauer is facing disqualification from this year's race, according to News Limited reports.
The report said European stayer Bauer, trained by Luca Cumani, was being investigated for treatment given to the horse in the lead-up to the race, which he collected $835,000 for his second placing behind Viewed.
The investigation will focus on electro shockwave therapy - commonly known as an ultrasound - the horse allegedly received on the Thursday prior to the Melbourne Cup, the report said.
Bauer was then under the care of Cumani, whose daughter Francesca had supervised the horse prior to her father's arrival in Melbourne.
Under Australian racing rules horses cannot race within seven days of receiving such treatment, which is designed to help healing.
Horses, however, can race within a day of treatment in Europe.
Racing Victoria Limited, which has placed a gag on all employees, has confirmed an investigation was taking place but did not reveal further details.
Bauer's win in the Geelong Cup will not be part of the inquiry, which will continue on December 11 when Bauer's managing owner Terry Henderson returns from England.
Any disqualification will not affect betting payouts as correct weight has already been declared.
Should Bauer be disqualified, each horse behind him would climb a place, leaving C'est La Guerre and Master O'Reilly as the minor placegetters.
The owners of Nom Du Jeu and Profound Beauty would also collect extra prizemoney, while connections of Ice Chariot, which finished 11th, would receive an $115,000 cheque whereas previously they would not have received a cent.
Any disqualification would also place RVL in an unenviable position as the body had spent considerable time and money luring horses from Europe for the Cup.
Connections are concerned by the investigation but feel they have done nothing wrong.
"We had a slight issue with Bauer and he (the vet) recommended the treatment," Cumani told Sydney radio station 2KY.
"We were told it was OK and we have to rely on the vet's advice."
"This treatment is widely available in every racing country. It is only banned in England on race day so I wasn't aware there would be an issue."
"The vet was appointed by Racing Victoria to look after our horses, I thought everything was fine."
"I took it for granted that if he recommended it, it would be OK."
"I probably should have looked at the rules myself and I was not aware this physiotherapy was not allowed."
Trainer Joe Janiak was punished for similar naivety in December 2006 when Takeover Target was a raceday scratching from the Hong Kong Sprint after being found to have a prohibited substance in his system.
The substance is not banned in Australia.