Whooping cough, a highly contagious bacterial disease characterised by fits of violent coughing, can lead to brain damage and death in infants in severe cases, but adults generally only suffer flu-like symptoms.
The AIS said the entire Olympic water polo team had been quarantined after team members Melissa Rippon and Nicola Zagame were both diagnosed with the disease.
"The water polo team is in camp at the AIS and has been placed in isolation to mitigate the risk of infection for athletes, staff and the public," the AIS said on its website.
"All members and officials of the team have been tested."
Australian Water Polo said both Rippon and Zagame would return to full training next week and were not in danger of missing out on the Games.
"Water Polo Australia is taking this very seriously and will continue to work closely with AIS health professionals to provide the best care for those players diagnosed and to reduce any potential further risk," the governing body said in a statement.
The outbreak prompted Swimming Australia to scrap a planned training camp for the team's Olympic relay swimmers and a Grand Prix meeting in Canberra this weekend as a precaution.
"We have spoken with the AIS and, whilst we are comfortable with the procedures they have put in place, we have decided to take this precaution," Olympic swimming head coach Leigh Nugent.
"Originally we'd planned to have this camp as an opportunity to come together for some further relay preparation and the chance for some of the athletes to race and time trial, a month or so out from the Games," Nugent added.
"From a relay perspective we are confident we're on track with our preparations and will fine-tune things when we get to Manchester in July.
"As for the racing side of things, I'm sure the individual coaches will arrange time trials if they see fit to replicate that preparation.