Biologists said in 2014 that rivers leading into Rio's Guanabara bay contained superbacteria that are resistant to antibiotics and can cause urinary, gastrointestinal and pulmonary infections.
The cleaning of its polluted waters was a key part of Rio's bid pledge to host the Summer Games and has long been a goal of successive local governments.
"We are very confident that the competition area for the athletes will offer safe and fair conditions," IOC president Thomas Bach told reporters.
"The city, the state and the organising committee are undertaking many efforts and what we see now is that 60 percent of the surface is clean. Without the Games it would be zero."
When Rio bid to host the 2016 Olympics, the city said it would cut the amount of raw sewage flowing into the bay by 80 percent but has since confirmed it will not meet that target.
"The last stretch is always the most difficult one and also there are challenges, but ... we're very confident (they) will be excellent Games," Bach said.
(Reporting by Karolina Tagaris; Editing by Gareth Jones)
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