The promoters of two big European athletics meetings said last week that U.S. anti-doping and track and field chiefs should suspend the two American sprinters until doping allegations against them have been settled.
Rogge said in a newspaper interview that he expects the case to be cleared up before the Athens Olympics in August.
"At the moment, the case of Jones and Montgomery does not exist as far as the IOC is concerned. You have to have evidence before you sentence somebody, and in the light of the law they are innocent," Rogge told Polish daily Rzeczpospolita.
"If the American authorities present evidence, both will be disqualified immediately. I believe the whole matter will be cleared up before the Games."
Montgomery, the 100 metres world record holder, and his partner Jones, the 2000 Olympic 100m and 200m
The U.S. Anti-Doping Agency (USADA), which is leading the investigation into Jones and Montgomery and other U.S. Olympic hopefuls, has yet to make any findings against the pair public.
Jones and Montgomery, who have never tested positive for a banned substance, have consistently denied any wrongdoing.
Turning to Olympic preparations, Rogge said the IOC had failed in the past to influence the pace of work, but added that he was now "100 percent certain" Athens would be fully prepared for the August 13-29 event.
"Two years ago, when we first received worrying signals about delays, IOC inspectors began to visit Athens to influence the pace of work. We were modestly successful, but in the 11th hour our Greek friends really rolled up their sleeves."