Banned for doping offences in 2004, Millar, who is working at the World Championships as a commentator for the BBC, questioned UCI President Pat McQuaid in a press conference in Holland.
The Scot refuted McQuaid's statement that the UCI had done all it could to combat doping in cycling. "We all know it was easy to beat the system," Millar said. "I was one of the people who easily beat the system."
During the exchange, Millar suggested to McQuaid that the UCI should take more responsibility for the drugs scandals of the past decade or so.
"I don't think so," McQuaid responded. "I don't see why we should be apologetic."
"We do more testing than anyone else," McQuaid told Millar. "If we got information at any point in time, we would act on that information. You did what you did, and you didn't rush to inform that to the UCI."
"Others doped and then spent small fortunes to tell the UCI and the world they didn't dope, only to later say they did. The UCI is not to blame for the culture of doping in the sport."
In fact, Millar did write at length to the UCI and the Tour de France organisation soon after making his comeback from his ban in 2006, voicing his concerns over doping within the team he had joined, Saunier Duval. The UCI did not respond to him.
"If it is apparent there was a black period," Millar said, "I think it's time for the UCI to say, 'maybe we didn't do everything we could have done, and we're sorry for that.' Now they're just saying, 'oh, we did everything we could, we have no regrets.' It was an era in the sport when doping was prevalent. It's something we all have to admit to now. It's not that we can just pretend it didn't happen. We're seeing now there are repercussions and that's a good thing."
Earlier, McQuaid denied the repeated claims made by Armstrong's former team-mates, Tyler Hamilton and Floyd Landis, both of whom have admitted to doping, that the UCI had covered up positive tests.
"The UCI has never hidden a sample of any rider, in particular of Lance Armstrong," McQuaid said. "In relation to other statements made by people that the UCI had informed Armstrong in advance of testing, that's a complete fallacy and completely ridiculous."
However, Millar also argued that cycling's culture of doping has largely been eradicated in recent years.
"The sport's changed incredibly," Millar said. "The bottom line is now you're a young guy coming into the sport today, you can win the biggest races clean. That was something unimaginable even a few years ago."
Millar, gold medallist for Scotland in the 2010 Commonwealth Games, said that the US Anti-Doping Agency (USADA) investigation into Lance Armstrong, which has resulted in USADA stripping the Texan of his seven Tour wins, is the "best thing for cycling".
"I really do believe that it could end up being for the best. It's a positive in the long run," Millar said. "We will no longer have these shadows lurking in the background and this confusion. I think we can all try to be on the same page now moving forward, which we would have never been without the USADA case."