The bacteria is normally found in hospital waste and can cause urinary, gastrointestinal and pulmonary infections, officials with the Oswaldo Cruz Foundation said on Monday.
They discovered the bacteria in water samples taken at three spots along the Rio Carioca, a small river that runs into the Guanabara Bay, where the sailing events will take place.
The bacteria is similar to other known strains but is resistant to the usual drugs, said Ana Paula D'Alincourt Carvalho Assef, the coordinator of the study that was published on the Oswaldo Cruz's website.
"There is the risk of contracting diseases, which are not more serious that those caused by other micro-organisms," Assef said, adding that no cases have yet been reported.
"The problem is that in case of infection it is possible that treatment involves hospitalisation."
Sailors who visited Rio for test events ahead of the Games criticised the state of the water, with some describing it as "filthy."
More than half the water that flows into the Guanabara Bay is sewage and organisers have vowed to reduce that amount by 80 percent by the time the events start in Aug. 2016.
(Reporting by Andrew Downie; Editing by Ian Ransom)
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