The disgraced American, stripped of his seven Tour titles because of blood doping, has been invited by fellow cancer survivor and former English football player Geoff Thomas to join him in raising money for a leukaemia charity.
"Lance Armstrong riding on some or all of the route one day before the race, I can't think of better words than disrespectful and inappropriate to the Tour de France, the current riders, the UCI and anti-doping," UCI chief Cookson told reporters at a sports industry meeting on Tuesday.
"The charity justification was used quite a lot throughout his career and that got us into all sorts of a mess which is well documented.
"It looks like Lance was persuaded into it and if he was it's not a good judgement. I think he would be well-advised not to take part in that."
"I've never met him or spoken to him on the phone or by email, I'm not unhappy with that situation but I think there's a message I'm giving out today," he added.
Cookson said he had "no authority" to stop Armstrong joining the charity ride while Thomas, who rode the Tour route 10 years ago after going into remission for chronic myeloid leukaemia, defended the Texan, saying he would only ride a few stages.
"At first he was suspicious, but I worked on him, told him about what the charity does, and he was intrigued," former England midfielder Thomas said.
"What I saw was somebody who was frustrated he couldn't do that type of work with LiveStrong anymore. It's a great opportunity to get him back into that realm, and hopefully in future help him make millions of pounds for charity again."
"I knew I'd get a reaction from people who may have not looked to deep into the story. I believe the positives will outweigh that as we go on."
Asked whether he had any sympathy for Armstrong, who is trying to have a life ban from cycling imposed by American anti-doping body USADA reduced, Cookson was unequivocal.
"He has been singled out and made an exceptional case but then there aren't many who have won the Tour de France seven times by cheating, so he was an exceptional case," Cookson said.
"I'm not anxious to be the president that brings Lance Armstrong back into cycling."
(Editing by Ed Osmond)
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