The investigation by the Cycling Independent Reform Commission (CIRC) slams the way the world body -- the International Cycling Union, or UCI -- operated over a lengthy period and calls for a series of changes to its governance.
The report highlights multiple instances in which top UCI officials protected, defended and made decisions favorable to Armstrong despite concerns that he was doping.
Current UCI president Brian Cookson, who was elected to his post in September 2013, told CNN Monday that he had written to one of his predecessors, Dutchman Hein Verbruggen, to "consider his position" as the honorary president of the world governing body in the light of the findings.
Both Zerbruggen and Irishman Pat McQuaid, who Cookson unseated, both come under intense scrutiny in the report for their dealings with Armstrong.
"UCI exempted Lance Armstrong from rules, failed to target test him despite the suspicions, and publicly supported him against allegations of doping, even as late as 2012," it says.
Armstrong seen as sport's savior
The UCI "saw Lance Armstrong as the perfect choice to lead the sport's renaissance" after a devastating doping scandal at the 1998 Tour de France, according to the report.
"The fact that he was American opened up a new continent for the sport, he had beaten cancer and the media quickly made him a global star," it says.
But Armstrong's spectacular downfall in 2012
, which saw him stripped of his Tour de France titles and dropped by sponsors, helped intensify scrutiny over how he managed to get away with doping for so long.
Under Cookson, the UCI set up the independent three-person commission to investigate the causes of doping in cycling and allegations that the UCI and other governing bodies were ineffective in their responses.
Interference in investigation
In one case, the commission says, the UCI limited the scope of a supposedly independent investigation into allegations that Armstrong had tested positive in a drug test at the 1999 Tour de France.
UCI officials and Armstrong's team became heavily involved in the drafting of the investigation's report, which was released in 2006.
"The main goal was to ensure that the report reflected UCI's and Lance Armstrong's personal conclusions," the commission says. "The significant participation of UCI and Armstrong's team was never publicly acknowledged."
Between 1992 and 2006, UCI's top officials focused on protecting cycling's reputation rather than trying to root out "endemic" doping practices of which they were well aware, the commission's report says.
"Not only did UCI leadership publicly disregard the magnitude of the problem, but the policies put in place to combat doping were inadequate," it says.
'A sudden U-turn'
The report highlights McQuaid's decision to allow Armstrong to participate in the 2009 Tour Down Under even though the cyclist hadn't been in the testing group for the required period of time.
The commission says although there is no direct evidence of an agreement between McQuaid and Armstrong, McQuaid "made a sudden U-turn and allowed Lance Armstrong to return 13 days early" to take part in the competition, "despite advice from UCI staff not to make an exception."
"There was a temporal link between this decision, which was communicated to UCI staff in the morning, and the decision of Lance Armstrong, which was notified to Pat McQuaid later that same day, to participate in the Tour of Ireland, an event run by people known to Pat McQuaid," the report says.
The report says the commission found no evidence to support allegations of corruption over payments made to the UCI by Armstrong.
But it adds that "requesting and accepting donations from Lance Armstrong, given the suspicions, left UCI open to criticism."
CNN wasn't immediately able to reach McQuaid, but Verbruggen issued a lengthy statement Monday, claiming "wild conspiracy theories and accusations have been properly debunked once and for all."
He said: "I have studied the CIRC report and I am satisfied that it confirms what I have always said: that there have never been any cover-ups, complicity or corruption in the Lance Armstrong case or, indeed, in any other doping cases."
Armstrong's support for investigation
Armstrong, who cooperated with the commission's investigation, thanked it for "seeking the truth and allowing me to assist in that search."
"I am deeply sorry for many things I have done. However, it is my hope that revealing the truth will lead to a bright, dope-free future for the sport I love," he said in a statement.
"In the rush to vilify Lance, many of the other equally culpable participants have been allowed to escape scrutiny, much less sanction, and many of the anti-doping 'enforcers' have chosen to grandstand at Lance's expense rather than truly search for the truth," said Armstrong's attorney, Elliot Peters.
The U.S. Anti-Doping Agency, USADA, which banned Armstrong from cycling for life in 2012, welcomed the commission's work.
"The report confirms that, for more than a decade, UCI leaders treated riders and teams unequally -- allowing some to be above the rules," said USADA Chief Executive Travis T. Tygart. "The UCI's favoritism and intentional failure to enforce the anti-doping rules offends the principles of fair play and is contrary to the values on which true sport is based."
UCI chief hits out at 'child abuse'
Cookson told CNN that the world governing body would be stepping up its fight against drugs cheats, working closely with the World Anti Doping Agency (WADA), national federations and, if necessary, law enforcement agencies.
But the 63-year-old Briton still believes cycling has taken strides forward in the fight against drugs cheats.
"Large numbers of riders are competing without doping," he said. "I want to encourage them and support them. I think it's possible to compete successfully in our sport without doping."
However, Cookson reacted angrily to other aspects of the report, which suggested amateur cyclists and junior competitors were involved in doping.
Of older cyclists, competing in Masters categories, Cookson gave a damning verdict. "The only people they are fooling is themselves, they are deluded," he said.
But his harshest words were reserved over allegations that drugs were being peddled to young cyclists. "The people involved should be subjected to criminal proceedings because that's child abuse. I'm astonished and appalled by those findings," he said.