This is a time when people from the AFL have to stand up and show real leadership, not let the back pages hang out there and murder a player from Essendon or Essendon themselves.
The three-time premiership coach said it was both "disappointing" and "disturbing" nobody from the AFL had made a public comment since the reigning Brownlow Medallist's revelations on Monday night.
Watson shocked the football community and his own club when he told Fox Footy's On The Couch program that he had been administered a substance he believed to be AOD-9604, an anti-obesity drug which is which is not approved for human use and banned by the Wold Anti-Doping Agency (WADA).
"We've heard from Essendon, we've heard from a lot of football clubs but interestingly enough the one massive surprise in my book is we haven't heard from the AFL at all," Malthouse said.
"I find that disappointing, disturbing.
"This is a time when people from the AFL have to stand up and show real leadership, not let the back pages hang out there and murder a player from Essendon or Essendon themselves. Let's get some clarity on issues."
AFL boss Andrew Demetriou had been on the front foot hitting the airwaves when the drugs scandal first rocked Australian sport in February but is yet to respond to the latest development.
Watson's comments have thrust the issue back into the public spotlight and re-focused attention on the futures of key Essendon staff, such as coach James Hird and long-time club doctor Bruce Reid.
There is also widespread debate whether Watson should be allowed to retain the Brownlow Medal, the AFL's highest individual honour, he won last year.
"The governance of the game is the AFL Commission and they endorse an administration to act on their behalf," Malthouse said.
"One would suspect that we're all waiting to find out exactly what the AFL are thinking at this stage, which is a direct reflection of the Commission.
"I haven't read anything, heard anything or seen anything so that covers most of the media with any reference at all to the AFL or its Commission.
"I think we need a leading light in the area. It can't be left to the media's opinion.
"Watson's statement that has left the football world thinking what is going to happen."
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