The Wallabies led the second Test for all of 79 minutes until Irish star Hugo Keenan crossed the whitewash at the death to break Australian hearts. In the lead-up to the decisive try, Welsh flanker Jac Morgan executed a brutal clean-out on Carlo Tizzano from a ruck. Tizzano fell backwards clutching his head, but Italian referee Andrea Piardi - and the TMO - found nothing illegal. World Rugby laws state that contact made above the shoulders at the ruck is not allowed.
Keenan's try sealed an epic 29-26 comeback victory and wrapped up the three-match series for the storied tourists.
"We've got the utmost respect for respecting the referee's decision," Waugh told the local media on Monday.
"But I do think there's a level of accountability and explanation that needs to come with that. And we look forward to that.
"My response is identical to Joe's [coach Schmidt] comments in the press conference. I played professionally for 13 years, and Joe's coached professionally for 20 years, and both our views, and all those organisationally, are very aligned with what Joe talked about in that post-match press conference. I look forward to World Rugby's response to it."
In his post-match comments, a furious Schmidt said the decision "doesn't live up to the big player safety push" being made by World Rugby.
The third and final Test between hosts Australia and the British and Irish Lions kicks off in Sydney on Saturday.