Dr Hugh Seward, president of the association, said he looked forward to the facts being revealed in the near future.
The association has also offered help to Melbourne if it needs to beef up its medical services after Dr Bates offered to stand aside until the investigation is complete.
"I'm concerned about his (Bates) reputation being tarnished without basis," Seward told AFL.com.au.
"I'd be concerned that he was being held responsible for actions that other people were also involved in and he is then being made a scapegoat."
He said that there was a potential that Dr Bates' reputation was being damaged by association and not necessarily through doing anything wrong.
Bates began as Melbourne's club doctor in 2012 after spending a year at North Melbourne in 2011.
He is also involved in research on the use of stem cell surgery to overcome injury outside his club activities. He is considered a leading figure in the field.
Bates offered to stand aside on Friday evening after AFL investigators interviewed him during the day.
He had been summoned to AFL House at 10.30am on Friday to answer questions and was understood to be distraught at finding himself subject to an investigation.
In a statement that night, Melbourne said Bates had been interviewed three times during an internal review headed by a suitably qualified director.
The director who conducted the review is understood to be David Thurin, a doctor who joined the Melbourne board in 2009.
It is unknown what information Bates provided during that process.
Melbourne however said its internal review had found no evidence that the supplements program at the club contravened any ASADA or WADA guidelines and there was no evidence that any player had been administered a banned substance at any time.
The AFL was 'stunned' at the 7:30 Report's revelations and CEO Andrew Demetriou said on Friday there appeared to be inconsistencies between the information it had received from Melbourne and the program's revelations.
The AFL said in a statement last Thursday night that it had approached the Melbourne Football Club after the investigation into Essendon was launched to ascertain the club's involvement with Dank and was provided with an explanation.
However, it said the matter had remained open as part of the "AFL's broader investigation into Mr Dank's activities with AFL clubs".
Gold Coast, Geelong and the Brisbane Lions outlined their previous dealings with Dank soon after Essendon became subject to the joint AFL and ASADA investigation.
On Monday, AFL investigators interviewed more members of Melbourne's football department as part of its ongoing enquiry into the club's pre-season supplement program.
The Demons' football manager Josh Mahoney, sports performance manager Neil Craig and elite performance manager David Misson were individually questioned in relation to the program.
All clubs have provided the AFL integrity department and its medical commissioners with an audit of its supplement program.
