"What we saw with Pita, I'm sad to say, is someone who cheated the system, someone who got [around] the rules," Baena told Stuff.
At the centre of the controversy is a series of roller-skiing events held in Bogota, Colombia late last year. To meet the Olympic qualification standard, Taufatofua needed to score under 300 points in at least five races. Four of Taufatofua's sub-300 performances were achieved in races against the same seven competitors. Two of those races were just 2.5km sprints — well short of the 15km Olympic distance — while the other two were 10km races.
Baena, who failed to qualify for this year's Games, said the way they got those points was "cheating".
"This was a fake race they organised between themselves only for these guys to qualify," Baenea told Stuff. "If you saw their results from the real competitions against the experienced guys, they do not have the level. They got really high points. It does not match what they did in these races in Colombia.
"It is not really a fair game."
The respected Wall Street Journal earlier reported the Brisbane-based Tongan had to learn cross-country skiing from scratch and that his quest to qualify for the Winter Olympics had seen him training on roller skis rather than in the snow.
Michal Lamplot, the FIS's media and project coordinator for cross country skiing, said in a statement to Stuff the organisation was reviewing its qualification standards for the next Winter Olympics following questions over the legitimacy of the results of some of the athletes.
"FIS is aware of some results inconsistencies of several cross country skiing athletes during the PyeongChang 2018 qualification period. We are currently looking at how we can improve/modify the cross country qualification process for the next Olympic Winter games in Beijing in 2022," the statement said.