Armstrong admitted years of systematic doping in an interview with chat show host Oprah Winfrey on Thursday but the American maintained he was clean when he made a comeback in 2009, 3-1/2 years after retiring.
However, WADA chief John Fahey told Britain's Daily Telegraph on Friday: "The evidence from USADA (United States Anti-Doping Agency) is that Armstrong's blood tests show variations in his blood that show with absolute certainty he was doping after 2005".
"Believe USADA or believe Armstrong? I know who to believe.
"It struck me that the statute of limitations under U.S. law might be relevant and Armstrong would not want to admit to anything in regards to his comeback that might be picked up under the U.S. criminal code," Fahey added.
Armstrong, stripped of his Tour wins and banned for life last year after a USADA investigation, said in Thursday's interview that if asked to participate in a truth and reconciliation commission he would be "the first man through the door".
But Fahey responded by saying Armstrong had recently declined to give evidence to USADA under oath.
"The USADA invited him to come clean and advised he would have to give evidence under oath and provide substantial assistance and, if he indicated the nature of the evidence - and he would have to name times, dates, people - there may be a consideration of reducing his life sentence to a term of years," Fahey said in the Telegraph.
"But he never came back, he went to Oprah instead and that indicates how sincere he really was. He wanted to control the way his story was told.
"This bloke is a cheat and did my view of him change after watching the interview? No," added Fahey. (Writing by Alison Wildey; Editing by Ken Ferris)
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