Bradley Wiggins's use of TUEs while with Team Sky, made public by cyber-hacking website Fancy Bears last year, raised uncomfortable ethical questions about riders competing after being taking prohibited drugs for medical conditions.
Wiggins, the 2012 Tour de France winner and Britain's most decorated Olympian with eight medals, retired last year under something of a cloud after it was revealed he had taken corticosteroid triamcinolone for asthma.
The Briton broke no anti-doping rules, however, and Boardman says the situation could have been avoided.
"I don't think the world governing body (UCI) is doing its job if they are allowing a situation where something is legal but not ethical," Boardman told Reuters at the London Cycle Show.
"We have focussed on the individuals but the people who govern what happens with TUEs have been allowed to sit in the background and let it trundle on.
"How did we get to the situation where something is legal but people don't feel it's moral?
"It's like tax evasion and tax avoidance. Just because you get away with it, doesn't make it okay."
Boardman said he only ever requested TUEs twice in his long career, once for low bone density and once while recovering from breaking his ankle in six places. Both were turned down.
He said riders needed to be protected from the rules.
"If everybody has got exercise induced asthma it doesn't seem to be right really. I just think the whole system needs tightening up. If you are not well you shouldn't be racing."
Wiggins's use of corticosteroid triamcinolone prior to the 2011 and 2012 Tours de France and 2013 Giro d'Italia was described as "ethically wrong" by former team-mate Nicolas Roche last year. Triple Tour de France winner Chris Froome also said "questions remained" about Wiggins's treatment for asthma.
Boardman said Wiggins had not ended his glittering career how he would have liked, but has some sympathy.
"Riders are doing all they can to push the limits to be the best they can be every day, that's their job," the 48-year-old Boardman said. "It's not fair to give them a situation where they can be legal and not ethical.
"I think all the teams need to talk to their riders and say, okay, we'll publish (the TUEs). That is clarity."
With his commentating duties on the Tour de France, in which he won three Prologues in 1994, 1997 and 1998, his passionate campaign to grow cycling numbers in Britain and improve safety and his booming bike business, Boardman takes a more long-range view of developments these days.
But having spent a decade with British Cycling after his riding career, part of it as head of research and development, Boardman is disappointed to see the organisation under fire.
Last year Shane Sutton quit as head coach following a discrimination row, prompting a UK Sport probe into a "bullying" culture in British Cycling's elite programme.
It has also been dragged into a UK Anti-Doping investigation into allegations of wrongdoing in the sport.
"What's been amazing is that nobody has stood up and said look we've got the most successful team of any sport ever," Boardman said. "Yes, you have things that go wrong in any business and you fix them. It's not a disaster by any means."