Rogge called the evidence against Armstrong "shocking" but said it will ultimately be a "good thing" that helps clean up the sport after a string of high-profile drug cases.
Some critics have called for cycling to be thrown out of the Olympics following the U.S. Anti-Doping Agency report that detailed systematic cheating by Armstrong and other riders and led the UCI to strip the American of his seven Tour de France titles.
"It would be unfair to penalize the huge majority of clean athletes by banning UCI from the Olympic Games and we believe there are a number of ways by which cheaters can be kicked out of the sport," Rogge said in an email response to media questions.
While the UCI has come under fire for not preventing the widespread use of EPO and blood transfusions in cycling, Rogge said the sport had done more than most in trying to combat the use of performance-enhancing drugs.
"Sadly the sport of cycling has often been involved in high profile doping cases and necessarily the UCI has always been at the forefront of the fight against doping, being one of the first sports to introduce biological passports and also conducting a record number of tests on cyclists all year round," Rogge said.
He said tougher sanctions would have a deterrent effect, noting that the IOC is pushing for stiffer penalties in the next version of the World Anti-Doping Code. Sanctions could include four-year suspensions and bans from Olympic competition.
"Ten years ago the UCI faced some limitations in the fight against doping — not enough out-of-competition tests, and the inefficiency or inexistence of tests," Rogge said.
Since then, he said, EPO testing has become more effective, tests have been developed for human growth hormone and homologous blood transfusions, and athletes' blood profiles are being monitored through the biological passport program.
"All these means which were not available in the past have significantly advanced the fight against doping and UCI was one of the first federations to implement them," Rogge said.
The USDA report described how Armstrong's teams used and trafficked banned drugs while the Texan dominated the Tour from 1999-2005. UCI President Pat McQuaid, whose position has also come under scrutiny, said Monday that Armstrong "deserves to be forgotten in cycling" as the federation ratified USADA's ruling to take away his Tour titles and ban him from life.
McQuaid is an IOC member. Former UCI president Hein Verbruggen, who was in charge at the time of Armstrong's victories, is now an honorary IOC member.
"The Armstrong affair comes as a real disappointment," Rogge said. "We were all aware of the stories in the press and the many rumours over the years. The fact that this is all finally coming to light with some blatant evidence is of course shocking, but ultimately this will be a good thing for the sport of cycling which has already started and will continue to prevent cheaters to compete, and more importantly work to protect the reputation of the sport for the sake of the young generations."
Rogge said the IOC will wait for the UCI's management committee meeting on Friday before possibly stripping Armstrong of his road time-trial bronze medal from the 2000 Sydney Olympics. The IOC must determine whether the eight-year of statute of limitations applies in the case.
"It would be premature for the IOC to make any comment before UCI says what it intends to do," Rogge said. "It is good, however, to see that all parties involved in this case are working together to tackle this issue."
The IOC will also consider removing Levi Leipheimer's time-trial bronze medal from the 2008 Beijing Games after he confessed to doping in his testimony against former teammate Armstrong.