Rogge's statement means Greek sprinter Katerina Thanou -- at the center of her own drug scandal at the 2004 Athens Games -- might not receive the 100-meter gold medal Jones won at the 2000 Sydney Olympics.
"This is not going to be an automatic upgrade. ... Every potential upgraded athlete will be scrutinized on his or her merits," Rogge said in a conference call. "We want to upgrade athletes if we are absolutely sure that they are clean. Every case will be examined."
Jones, who won three gold medals and two bronze in Sydney, admitted in October to using performance-enhancing drugs before the 2000 Olympics.
The medals were returned to the IOC, which is awaiting recommendations from track and field's governing body, the IAAF, to disqualify Jones before stripping her of her titles.
Jones won golds in the 100 meters, 200 meters and the 1,600 relay in Sydney, as well as bronzes in the 400 relay and long jump.
Under standard procedures, the medal standings are adjusted so the silver medalist moves up to gold if the winner is disqualified for doping or other reasons.
However, the IOC and IAAF are in the awkward position of dealing with the possibility of Thanou being bumped up from silver to gold in the 100.
Thanou and fellow Greek runner Kostas Kenteris failed to show up for drug tests on the eve of the Athens Olympics, claimed they were injured in a motorcycle accident and eventually pulled out. Both later were suspended for two years.
Finishing behind Jones and Thanou in the 100 was Tanya Lawrence, with fellow Jamaican Merlene Ottey in fourth.
Pauline Davis-Thompson of the Bahamas won the silver behind Jones in the 200, with Sri Lanka's Susanthika Jayasinghe third and Jamaica's Beverly McDonald fourth.
The IOC is also waiting for a recommendation from the IAAF on removing the medals from Jones' American relay teammates.