An investigation has revealed water in the city of South America’s first ever Olympic games is contaminated with human waste, making it a serious health concern for athletes.

The Associated Press found the water where swimming and boating events will take place at the 2016 Rio de Janeiro games is full of alarming levels of bacteria and viruses.

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Garbage floats in the Cunha canal which flows into the notoriously polluted Guanabara Bay, site of sailing events for the Rio 2016 Olympic Games Photo: Getty

Despite the test results, an Olympic official told AP that there are no plans to address or monitor the problem.

“The results have alarmed international experts and dismayed competitors training in Rio, some of whom have already have fallen ill with fevers, vomiting and diarrhoea,” Associated Press reported.

“These ailments could knock an athlete out for days, potentially curtailing Olympics dreams and the years of hard training behind them.”

One athlete who has already trained in Rio’s Guanabara Bay for months has fallen ill.

“I’ve had high temperatures and problems with my stomach,” Austrian sailor David Hussl said. “It’s always one day completely in bed and then usually not sailing for two or three days.”

His coach, Ivan Bulaja went further by saying: “This is by far the worst water quality we’ve ever seen in our sailing careers.”

“I am quite sure if you swim in this water and it goes into your mouth or nose that quite a lot of bad things are coming inside your body.”

The Rio de Janeiro environmental agency said in a statement it questioned the AP’s testing. It accused the virologist who carried out the testing and his university as “seeking notoriety”.

AP report it is not paying the the virologist, Fernando Spilki, for the testing. He is a board member of the Brazillian Society for Virology and edits its scientific journal.

The environmental agency say all competitions areas are safe, except for Marina da Gloria, where sailing competitions begin.

However the Brazilian government’s own water testing shows that on June 25 water at the famous Copacabana Beach was above legal bacteria limits.

This means it is unsafe for bathing. The medical director of the International Olympic Committee says the IOC has had assurances from the World Health organisations and “others”, that there is no significant risk to the health of athletes.

He said athletes should wash their hands to avoid or reduce the risk of infection after swimming in what AP describes as “virus-laden” waters.

Olympic competition gets underway in August 2016, but experts say it is too late for a clean up.