Melbourne announced on Friday night it had accepted Bates' offer to stand down from his position immediately pending the outcome of an investigation by ASADA and the AFL into the club's pre-season supplements program.
"We have sufficient concerns about an identified breakdown in reporting protocols that we believe it is appropriate that Dr Bates stands aside until these matters are further investigated," Melbourne president Don McLardy said.
Melbourne said it conducted an internal review of its supplements program after the announcement of the ASADA investigation into Essendon in February, which had included three interviews with Bates.
The club said the review had revealed no evidence that any player had taken a banned substance.
Earlier it is believed Bates and Melbourne football manager Josh Mahoney attended a marathon meeting at AFL House over reports of their alleged involvement with Dank.
The meeting was scheduled to begin at 10.30am and didn't conclude until after 5pm.
"Can't make any comment at this stage, the club will say something when it can," Mahoney told reporters as he left AFL House.
Earlier, AFL chief executive Andrew Demetriou said claims on the ABC's 7.30 current affairs show that it had text messages between Bates and Dank were inconsistent with what Melbourne had told the AFL.
"They had maintained a position ... that they've never employed Stephen Dank," Demetriou told ABC radio on Friday morning.
"If there is an association with Mr Dank, that is inconsistent with what we have been told.
"We will get to the bottom of it and if there is anything there that is inconsistent with what we have been told, we will tackle it then."
The ABC's revelations are certain to lead to the Australian Sports Anti-Doping Authority (ASADA) and the AFL widening the probe into supplement use to include the Demons.
Demetriou said Melbourne had some questions to answer if the ABC report was true.
"As of this morning we will be calling in the doctor, the Melbourne Football Club doctor, together with any other relevant officials based on things we'd been told previously," Demetriou said.
"There appears to be some inconsistencies.
"If there was an association, regardless of whether there has been an employment agreement, I think that would have been relevant to our briefings."
Demetriou did not want to speculate on the ramifications for the club if it was shown to have misled the AFL about a relationship with Dank.
"This issue of ethics and trust in our code ... is something that you can't play ping-pong with," Demetriou said.
"If anybody hasn't got the message that they must be absolutely truthful ... then there will be consequences."
Demetriou said it would have been a more sensible and appropriate course for Melbourne to inform the AFL of the extent of their relationship with Stephen Dank so they could avoid any "potential situations down the track."
Demetriou did not comment on whether it had shaken his belief in the primary role of the doctor in administering supplements but said that Bates was entitled to explain himself.
He did not think there was any need to recall AFL clubs for a further briefing in the light of the alleged revelations in relation to Melbourne.
In a lengthy statement on Friday morning, Melbourne said there was no evidence any of its supplements breached the WADA drug code, and that Dank never directly treated players nor worked directly for the club.
Demetriou said that the appointment of Peter Jackson as the Demons interim CEO on Thursday was very important and gave him confidence of the club's ability to manage the situation.
"He'll know exactly how to tackle this issue on behalf of the club," Demetriou said.
He said it was possible ASADA were not aware of the alleged text messages revealed on 7.30 on Thursday night.
Although he acknowledged the potential damage to the game's image, the AFL CEO said the organisation had acted quickly to deal with the issue and keep investigating the issue to rid it of unsuitable practices.
"We are going to find out things during that process. We shouldn't stop. We have got to keep pushing forward to protect the integrity of the game," Demetriou said.
