McQuaid was the UCI President until September 2013, when he was ousted by Brian Cookson, and he has had no qualms about criticising Team Sky since leaving his post.
McQuaid reiterated his views to Cyclingnews that Team Sky "went further in the grey areas than marginal gains. I think it was going against the ethics of the sport and I disagree with that."
Speaking to the BBC yesterday, Wiggins denied any wrongdoing and said, "Not at any time in my career did we cross the ethical line."
However, McQuaid dismissed Sky Team Principal Dave Brailsford's repeated assertion that Sky did things "the right way."
"The sad part is that Team Sky's success came after many doping scandals, including Lance Armstrong," McQuaid said. "Sky always said that they were whiter than white, that it was all within the rules and down to marginal gains, to diet, pillows and mattresses. Now we know that wasn't the whole story.
"They were misleading people," the Irishman said. "In their statement this week, they recognised that mistakes were made, and to me they must accept that they misled people."
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McQuaid said that the exploitation of grey areas was also a characteristic of British Cycling and cited the example of a crash involving Chris Hoy at the UCI Track World Championships in 2009 and his conversation with British Cycling staff afterwards.
"I said to them, 'That must have been a very expensive crash', because the bikes were wrecked — they told me it was £15-20k worth of damage," he recalled.
"I was very concerned to hear that because under UCI rules the bikes were supposed to be commercially available, but these were specially made bespoke machines.
"I spoke to Brian Cookson, who was BC President at the time, and said it wasn't acceptable. A few months later the bikes appeared on sale online."
But McQuaid also said that he had not been aware of any specific details of Team Sky's usage of TUEs during his time as UCI President.
"TUEs sat with the UCI's medical team, but there were so many coming in and coming in so often," McQuaid said. "The system was unsatisfactory. That goes across all sports not just cycling.
"It's important to say that the report wasn't just about cycling but also athletics. It shows a weak anti-doping system within sport, not just cycling. I always said that the TUE system was weak. Yes, there was too much use of corticosteroids, and I did try to do something about it.
"The problem is that the UCI can do very little about it as no UCI rules have been broken and no WADA rules have been broken. I pushed WADA on TUEs when I was UCI President, but the system is easy to get around."
McQuaid argued that the DCMS report's findings on British Cycling and Team Sky were an inevitable consequence of what he called the "gold rush that started before 1998."
"There was a pressure to win medals and get results, and I think there was a mentality of winning at all costs," he said.
Asked about the ongoing impasse on the investigation into Chris Froome's AAF for salbutamol, McQuaid was as scathing as Tour de France director Christian Prudhomme earlier this week, when the Frenchman described the situation as "completely farcical."
"The Froome case may well be the nail in the coffin for Team Sky," McQuaid said. "They will try and sit it out, but a lot depends on the result of the Froome case. But I can understand why ASO are spitting teeth, because it [Froome's case] should have been concluded by now."
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