The Federation Internationale de Natation (FINA), however, ruled the Russian synchronized swimming team, divers and the women's water polo team are still eligible to participate because they have not been implicated in the ongoing doping scandal.
The International Olympic Committee left the decision on competitors' eligibility up to their respective sporting federations, the IOC said in a statement
Last week,a damning report alleged a complex system of subterfuge furthered doping among Russian athletes. Russia's security services tampered with sealed urine samples, said the World Anti Doping Agency (WADA).
The scheme was directed by the country's sport authorities to cover up doping across a "vast majority" of winter and summer sports, the report stated, leading for a call to ban Russia from the Rio Games, which begin August 5.
Federations "should carry out an individual analysis of each athlete's anti-doping record, taking into account only reliable adequate international tests ...to ensure a level playing field," the IOC statement said.
"This is about doing justice to clean athletes all over the world. In this way we protect these clean athletes," IOC President Thomas Bach said Sunday in a call to reporters.
Russia's Olympic minister, Alexander Zhukov, said the IOC had come to "a well-considered decision which allows our athletes to compete in the Olympics under the Russian flag" despite pressure against them from the Western media.
Travis Tygart, head of the U.S Anti-Doping Agency (USADA), slammed IOC for "passing the baton" to sports federations, which he said may lack expertise or will to address the situation.
"In response to the most important moment for clean athletes and the integrity of the Olympic Games, the IOC has refused to take decisive leadership," Tygart said in a statement posted on the USADA Twitter feed.
Despite the IOC's ruling, Russia remains suspended from track and field events in Rio by the International Association of Athletics Federations (IAAF), a decision that was upheld by the Court of Arbitration for Sport
That suspension was introduced in response to a previous independent WADA report on doping last year.
Russia finished atop the medal standings at the Sochi Winter Games in 2014, securing 33 medals, including 13 gold. Two years before at the London Summer Games, Russian athletes won 79 medals, of which 22 were gold.
In a statement released Monday, WADA called on the IOC and the International Paralympic Committee to decline all athletic entries, for Rio 2016, from the Russian Olympic Committee (ROC) and the Russian Paralympic Committee."