Verbruggen, who headed the UCI during Armstrong's domination of the Tour de France, said the federation's policy was part of a "two-pronged attack" on doping at a time when it had an "impressive" record of catching drug cheats.
"It used to be the UCI's policy and indeed also of other federations to discuss atypical blood test results, or other test results, with the riders concerned," Verbruggen said in a statement provided to The Associated Press.
"Riders who were doping (but who had yet to fail a test) were effectively warned that they were being watched and that they would be targeted in future with the aim of getting them to stop doping," he said. "However, if the atypical test results were genuinely not caused by doping, the rider also had the opportunity to have a medical check."
Verbruggen, who is the UCI's current honorary president, issued a statement after Dutch magazine "Vrij Nederland" reported his comments that Armstrong and other riders were contacted about doping suspicions.
Armstrong's suspicious sample with traces of EPO at the 2001 Tour of Switzerland led the UCI to set up a meeting with the laboratory director who oversaw the analysis to explain how the test worked.
Armstrong and his team manager, Johan Bruyneel, then met Lausanne lab head Martial Saugy in Luxembourg ahead of the 2002 Tour. Saugy has said the meeting came several weeks after Armstrong returned another suspicious sample at a Tour warm-up race, the Dauphine Libere, in France.
The Dutch magazine reported that rider Karsten Kroon also met with UCI officials in 2004.
"First, it was not Hein Verbruggen who contacted riders," his statement said. "Instead, it was the UCI's medical advisers."
The UCI's former policy was formed "after some considerable debate and deliberation," Verbruggen's statement said. "Its purpose was to protect clean riders against competitors who might be doping, rather than to let those clean riders continue to be put at a disadvantage until such time that the drug cheats could be caught.
"It was intended to be a two-pronged attack on doping: prevention both by dissuasion and repression."
The magazine released extracts of its interview Tuesday, after French newspaper Le Monde published a doping control document relating to Armstrong's positive test for a corticosteroid during his first Tour win in 1999.
Armstrong, who has been stripped of his seven Tour titles and banned from elite sport for life, admitted to talk-show host Oprah Winfrey last week that he used a back-dated prescription to avoid sanctions for doping. He said the drug was a cream to treat saddle sores.
However, Le Monde's evidence suggested the UCI should have disqualified Armstrong anyway for breaching its rules requiring declarations of therapeutic use of substances. Armstrong and Bruyneel signed the doping control document which stated that he was not taking any medication at the time.
Verbruggen, who led the UCI from 1991-2005, insisted the governing body had "always been" a pioneer in sports' fight against doping.
"At the same time, the UCI's impressive record of catching riders through positive tests shows that cycling's governing body was not in any way soft on cheats," his statement said.