A report by the Independent Reform Commission published on Monday said previous UCI management were more concerned about their own image rather than tackling doping as the American rode his way to Tour de France glory from 1999-2005.
"The style of leadership is pretty much criticised in the report and led to major errors," Brian Cookson told reporters from the UCI headquarters in Aigle, Switzerland.
He added that the UCI was "trying to control and limit rather than eliminate (the problem) completely and at the time they always put the image and the business of the sport before integrity, transparency and honesty."
The then UCI management's shortcomings were first exposed in 2012 when the U.S. Anti-Doping Agency (USADA) published their reasoned decision after banning Armstrong, who later admitted to cheating, for doping.
"UCI exempted Lance Armstrong from rules, failed to target test him despite the suspicions, and publicly supported him against allegations of doping," the report said.
"The report confirms that, for more than a decade, UCI leaders treated riders and teams unequally, allowing some to be above the rules," USADA president Travis Tygart said in a statement.
It helped Armstrong cheat his way to Tour de France triumphs, according to Cookson.
"Clearly, a rider like Lance Armstrong, in 1999, had a positive test for cortisone (during the Tour de France) and UCI assisted him in covering that up," the Briton, who was elected in 2013, said.
"That was in my view an absolute critical moment."
After providing authorities with a backdated Therapeutical Use Exemption (TUE) following a positive test for cortisone, Armstrong continued and won the race, which had been labelled the "Tour of Renewal" one year after the Festina doping scandal.
The UCI is now taking the problem "seriously while other sports are not taking it seriously," Cookson added.
The UCI boss has a lot on his plate, however, as the CIRC report showed that doping, if less prevalent, is still endemic, with banned doctors still operating.
"These things are very difficult for a governing body (to fight against)," Cookson admitted.
"We'll work closer with governments."
(Reporting by Julien Pretot; Editing by Patrick Johnston)
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