If Scotland votes to break away from the United Kingdom, Scottish athletes who competed for Britain at the 2012 summer Olympics in London would not be eligible to do so with that country in Rio.
"We respect democratic decisions. We always do. But you can see from previous decisions we have been taking in similar cases that we are always safeguarding the interests of the athletes," IOC President Thomas Bach told Reuters.
In order for Scottish athletes to compete under an independent flag in Brazil in less than two years time, should they vote in favour of independence, they would need a national Olympic committee (NOC).
For that to happen and for the NOC to be recognised by the IOC it would first require a United Nations recognition of the independent nation of Scotland.
The rival campaigns in Scotland's fight over independence are running neck-and-neck nine days before the referendum, with a surge in support for those who wish to break away from the UK.
The number of people saying they would vote "No" to independence had dropped to 39 percent, down from 45 percent a month ago. "Yes" support was slightly behind at 38 percent but had gained ground from 32 percent a month ago.
More than four million Scots and residents of Scotland are eligible to vote in next week's referendum.
Tennis player Andy Murray, cyclist Chris Hoy and rower Katherine Grainger were among the Scots who won gold medals for Britain in 2012.
The IOC has options for athletes, whose nation's status as independent is not yet officially ratified with athletes in the past competing in the Games under the Olympic flag.
Athletes from the former Yugoslav Republic of Macedonia for example competed at the 1992 Barcelona Games under the Olympic flag with their national Olympic Committee not yet in place.
East Timor athletes did the same in 2000 with their country in transition to independence, as did a South Sudanese athlete at the 2012 Games.
Indian athletes also marched in the opening ceremony of the 2014 Sochi Winter Games under the Olympic flag with their country at the time banned from the Olympics over problems with an election process.
(Reporting by Karolos Grohmann, editing by Pritha Sarkar)
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