Organisers have vowed to improve the water quality to ensure the safety of athletes, including through installing underwater screens at Odaiba Marine Park to limit the amount of faecal coliform bactria flowing from offshore during rainy periods.
They also said they would consider amending event dates and times during the Games in response to weather conditions.
"We will take the best possible measures to make sure that the venue satisfies all relevant standards of international federations and that athletes can perform at their best feeling very safe," Koji Murofushi, Tokyo 2020 sports director, told a news conference.
Tests carried out during 26 days between July and September showed that water quality standards set by the international federations were met on only 10 days for marathon swimming and just six days for triathlon.
For example, the quantity of faecal coliforms tested on one day as high as 7,200 per 100 millilitres, well above the limit of 1,000 per 100 ml agreed by the International Swimming Federation.
Meanwhile, escherichia coli (E. Coli) tested as high as 5,300 per 100 ml, compared with the International Triathlon Union's ceiling of 250 per 100 ml, the Tokyo 2020 organising committee and Tokyo Metropolitan Government (TMG) said in a statement.
Faecal coliforms come from human and animal waste and a large amount could indicate illness-causing bacteria is also present, while some strains of E. Coli can cause diarrhea or illness.
BLAME THE RAIN
Tokyo officials laid much of the blame on a near-record 21 straight days of rain in August, saying the water quality at Odaiba varies significantly depending on the weather, and expressed confidence they could control the situation.
Still, they acknowledged the water quality already needed to be improved around Odaiba Marine Park, which is in a popular tourist district on Tokyo Bay.
From 2010 to 2012 they experimented using underwater screens, which they said were effective in reducing faecal coliforms, although the screens were not tested for effectiveness against other bacteria and are no longer in use.
"The experiment was completed in three years and based upon those results the TMG is considering what measures to take," said Kazuyuki Suzuki, a senior 2020 Games division director at the Tokyo Metropolitan Government, when asked why the screens had not been used for the past five years.
Tokyo officials also said they were working to increase the storage capacity of a Tokyo Bay sewage treatment facility.
International Olympic Committee (IOC) Vice President John Coates discussed the water quality issue with organisers during a regular project review meeting in Tokyo this week.
He said the IOC would be looking for how Tokyo plans to address the matter so that "the health of the athletes in those two sports will not be prejudiced in any way."
(Reporting by Chris Gallagher; editing by Ken Ferris)
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