Though Armstrong's exposure as a drug cheat was effectively sealed when the UCI on Monday ratified USADA's sanctions against the American, the two bodies have been quick to hurl accusations and critiques at one another.
UCI president Pat McQuaid conceded cycling was in crisis at a news conference on Monday, but he has since called into question USADA's evidence and methods while raising grounds for a possible appeal by Armstrong.
In a 'Decision' document posted on UCI's website and signed by McQuaid, USADA's report was said to have included "animated or overstated language" as well as "incorrect and incomplete statements".
"It would have been better that the evidence collected by USADA had been assessed by a neutral body or person who was not involved in collecting the evidence and prosecuting the defendant," the document said.
"This would have avoided both the criticism of (a) witch hunt against Mr Armstrong and the criticism that the UCI had a conflict of interest."
USADA chief executive Travis Tygart, who on Monday had called for a full and independent investigation into professional cycling, has since heaped further blame on UCI.
"The truth is Lance Armstrong, on their watch, pulled off the greatest heist sport has ever seen," Tygart told the Guardian.
"Instead of attempting to explain or justify their inadequacies, the UCI should acknowledge their responsibility and failures and find ways to make it right."
In response to UCI's suggestion that USADA should have handed over its case file for an independent body to open disciplinary proceedings, Tygart said: "We set forth our position on why they were conflicted in this case on many different grounds.
"They accepted money from him (Armstrong), they accused us of a witch-hunt (without seeing any evidence), they sued the chief whistleblower, they discouraged witnesses from participating.
"They simply are trying to divert attention away from their own failures in this whole sad saga, and those that love the sport of cycling and clean sport should not allow that to happen."
Armstrong, 41, had previously elected not to contest USADA charges, prompting USADA to propose his punishment pending confirmation from cycling's world governing body.
Former Armstrong team mates at his US Postal and Discovery Channel outfits, where he won his seven successive Tour titles from 1999 to 2005, testified against him and themselves and were given reduced bans by the American authorities.
McQuaid, who has been widely criticised for his and the UCI's handling of the Armstrong affair, was lambasted by World Anti-Doping Agency chief John Fahey earlier on Tuesday.
"Looking back, clearly the doping was widespread," Fahey told Fox Sports.
"If that doping was widespread, then the question is legitimately put: who was stopping it? Who was working against it? Why wasn't it stopped?" Fahey said the UCI had to "take the blinkers off" while asking a range of pertinent questions.
"Look at the past, examine the people who are there, ask themselves the questions 'Are those same people still in the sport and can they proceed forward with those people remaining?' "I don't think there's any credibility if they don't do that. I think they need to get confidence back into the sport so that its millions of supporters around the world will watch and support the sport going forward," Fahey added.
Tyler Hamilton, whose testimony helped bring down Armstrong, also blasted McQuaid, saying the Irishman had "no place" in the sport.
McQuaid had described Hamilton and Floyd Landis, who also testified against Armstrong, as "scumbags" on Monday.
"Pat McQuaid's comments expose the hypocrisy of his leadership and demonstrate why he is incapable of any meaningful change," Hamilton wrote in a statement on Tuesday.
"Instead of seizing an opportunity to instil hope for the next generation of cyclists, he continues to point fingers, shift blame and attack those who speak out, tactics that are no longer effective. Pat McQuaid has no place in cycling."
Hamilton and Landis were among the 11 former Armstrong team mates to testify against him.
Armstrong, widely accepted as one of the greatest cyclists of all time given he fought back from cancer to dominate the sport, has always denied doping and says he has never failed a doping test.