"Did I give the keys to get around EPO (erythropoietin) tests? The answer is clear: no," Martial Saugy, head of the anti-doping laboratory in the Swiss city of Lausanne, told a news conference.
The head of the USADA, Travis Tygart, claimed in an interview broadcast on Wednesday that Saugy tipped off the Texan rider about a test for the illegal blood booster in 2002.
That followed a "suspicious" sample the cyclist had given after the 2001 Tour of Switzerland, he told CBS television, adding that Saugy had told him that Armstrong had given samples that indicated EPO use.
Tygart also said the Swiss lab chief told him that world cycling's governing body asked him to meet Armstrong and his former manager Johan Bruyneel to explain the EPO testing process, calling the rendezvous "totally inappropriate".
Saugy on Friday confirmed that the International Cycling Union (UCI) had asked him to meet the pair.
However, "In the context I remain persuaded that it was the thing to do," he said.
"It was neither an error nor naivety as some people have written."
It would be "paradoxical" that the lab that found the first cases of EPO use should be the one to meet the race champion to tell him how to get around the test, he said.
"Our objective at the laboratory is anti-doping tests," he added.
Armstrong was banned for life from cycling and stripped of his seven Tour de France wins after the UCI confirmed a damning USADA dossier that placed him at the heart of what they said was the most sophisticated doping programme in sport.
Tygart said that six of cancer-survivor Armstrong's samples taken during his first Tour win in 1999 eventually tested positive when they were looked at again in 2005.
Armstrong, 41, continues to deny the allegations but is to appear on the Oprah Winfrey chat show in the United States next week, prompting speculation that he could own up to mitigate his ban and make a return to competition in triathlon events.