The Wallabies' hopes of avoiding a first ever opening-round exit are hanging by a thread despite Sunday's 34-14 win over Portugal, who they now need to beat Fiji next weekend without allowing the Pacific islanders a bonus point.
"It's been bitterly disappointing," former test flanker Waugh told reporters in Saint Etienne.
"I think we came here with a lot of hope and optimism and where we sit here now, everything's out of our hands, ... very disappointed with the journey to where we are today. And we've got a lot of work to do."
Waugh said Rugby Australia would review the campaign but his gut feeling was that the problems with the game Down Under ran a lot deeper than coaching and team selection.
"Where we are now, praying for a Portugal win, the performances certainly weren't at a level that they needed to be when it comes to World Cup," he added.
"There's a lot that's been declining across Australian rugby for some time and I think it's really important for us to sit back and say, 'how can we improve the overall ecosystem so that we can produce players that can compete on the top stage?'"
Waugh said his expectation was that Jones would stay on after the tournament and fulfil his contract through to the end of the 2027 World Cup, which Australia will host.
"We're committed to Eddie in the commitment we made to him earlier in the year," he said. "We'll go through the assessment of this campaign, but I think the most important thing is to look at the overall structure of Australian rugby.
"Our intent is to continue on the path that we're on," he added. "I think this is not so much around chopping and changing coaches as it is around actually just fixing the system."
With only two years until the British and Irish Lions tour Down Under, Waugh said that time was of the essence and Rugby Australia had to deliver on the plan announced in late August to reset the game from top to bottom.
"What we haven't done over time is delivered what we've said we're going to deliver," he said.
"So whilst we have this great vision, what's really important is actually to build trust with our stakeholders in our member unions to believe that we can deliver on the vision."