Armstrong alleged collusion by Verbruggen during his first Tour victory in an interview published Monday in Britain's Daily Mail.
After urine samples showed traces of a banned corticosteroid, Armstrong's team produced a backdated prescription for a saddle sores cream. He was allowed to continue riding toward a victory which revived the sport's popularity after damaging doping scandals.
"It's a ridiculous story and, in addition to that, it was not a positive (doping) case," Verbruggen told The Associated Press in a telephone interview. "He must have reasons to come up with these allegations. I don't know what ... maybe to do with his court cases."
Verbruggen did say he spoke to Armstrong at the time.
"I might have told him that the UCI needs a prescription but I am sure that was handled by our anti-doping department, not me," he said. "According to our rules, it (the prescription) could be done afterwards."
Armstrong had declined to implicate the UCI during his interview with Oprah Winfrey in January, in which he admitted extensive doping, including with cortisone, during his seven Tour wins.
In this week's Daily Mail interview, he claimed Verbruggen instigated a coverup to explain his positive tests at cycling's signature race, which had been wrecked by doping cases in 1998.
"The real problem was, the sport was on life support," Armstrong was quoted as saying. "And Hein just said, 'This is a real problem for me, this is the knockout punch for our sport ... so we've got to come up with something.'"
Verbruggen said cortisone ointment had been permitted.
"It was a cortisone shot that was not allowed," he said, adding that the pattern of Armstrong's tests on four different days was consistent with using a cream.
The explanation was accepted by French authorities, who held responsibility above the UCI for anti-doping at the race, Verbruggen said.
Verbruggen served as UCI president for 14 years, stepping down in 2005 after Armstrong's seventh straight Tour victory.
Armstrong's coverup allegation is expected to be studied by an independent panel being set up by the UCI's new leadership to examine the governing body's past links with the rider and establish if he was protected from scrutiny.
"I have never been afraid of any investigation commission," Verbruggen said. "I will participate in everything and I will be never be found (guilty of) anything."
Verbruggen, the UCI's honorary president and an IOC honorary member, is a likely target witness for the independent commission which newly elected UCI President Brian Cookson said in Johannesburg last week could begin work early next year.
"What I am really interested in, I have to say, is the allegations (Armstrong) has apparently made ... about the way in which he was given special treatment by the UCI. If that was true, I'd like to know about it," Cookson told the AP at the World Anti-Doping Agency conference.
Armstrong is expected to be the star witness and has suggested he wants a reduction in his lifetime ban. It was imposed last year by the U.S. Anti-Doping Agency, which also stripped his Tour victories.
Verbruggen suggested that the rider was "pulling your leg" when stating his willingness to co-operate.
"He wants a 'Truth and Reconciliation Commission.' He wants a commission to find out that he was not the only one (doping), and that he was forced to do it," the former UCI leader said.