Worries about the venue initially focused on the 500 crocodiles that live in and around the river but there are also concerns about the impact of river current on the fairness of competition and the lack of accommodation in the city of 80,000.
Queensland Premier David Crisafulli, however, announced in state parliament on Thursday that an independent technical review had found the course capable of hosting fair rowing and canoeing competitions in 2032.
Experienced coaches and former elite rowers remain unconvinced that a venue some 600 km north of the host city is the best option.
"Without a massive infrastructure spend, it's just going to be like a country regatta with Olympic athletes," former world championship medallist Andrew Butler, who has coached rowing for 17 years, including on the Fitzroy River, told Reuters.
"Why are you taking it 700 km away from a multi-sport event when it's obviously not to a better venue?"
Three-times Olympic champion Drew Ginn said he had concerns that water depth, river characteristics and the potential for flooding could all impact the competition.
"I row on a river in Melbourne. I love rowing on it, love training on it, but I'd never want to compete at the Olympic Games on it," he told Reuters.
"If you have flowing and moving water, that is completely unfair. One lane over another lane can be dramatically different. Imagine if (a flood) happens the week of the competition. Races get cancelled or the venue has to be moved.
"There's never been a national championships held there, there's a reason for that. It feels like it's a gamble that the Queensland government's taking."
Ginn also called for the technical review to be made public.
"If there's good evidence for it and good data for it, then you should be able to make it transparent," he added.
In a press release issued by Brisbane 2032 organisers on Thursday, World Rowing President Jean-Christophe Rolland was quoted as saying the venue could deliver fair competition but unusually the body did not issue its own statement nor the report.
There was no immediate response from World Rowing to a Reuters request for comment on the technical endorsement.
In a short statement, Rowing Australia "acknowledged" the completion of the technical review while making it clear neither it nor Rowing Queensland had played any part in the process.
John Driessen, an Olympic rowing coach and former elite rower who has coached on the Fitzroy River, echoed Butler and Ginn's concerns over the legacy of the venue.
"I've coached at Fitzroy and it worked really well. But turning it into an Olympic-class course, I would have thought would be quite expensive and difficult," he told Reuters.
"There'd be a lot of money going into a spot where there's no real guarantee that it would benefit the state of Queensland in the future."
Driessen said he did not think the Fitzroy River course would necessarily lead to unfair competition, however.
"It's quite a shallow course," he said.
"If they're going to maintain the basic principles of a rowing course with depth and lack of flow, then I think it would be a challenge to achieve that.
"(But) I'm not sure that if the course was run at Rockhampton, it would be that unfair in terms of lanes."
Driessen said hosting the Olympic rowing at Moreton Bay just north of Brisbane, the site favoured by Rowing Queensland, was a "no-brainer" and "the simple answer".
Butler favoured the original plan to stage the rowing on flat water at Wyaralong Dam some 86 km southwest of Brisbane, describing it as "probably the best course I've rowed on in Queensland".
"Investment there would be an absolute legacy ticket," said the twice Australian champion.
Crisafulli is determined, however, that regional cities around Queensland should be able to share in the Olympic experience and has previously denounced critics as "elitist".
"I thought the Olympics was a sporting event," said Butler.