Swimmers will stay in their home states to prepare before the first group heads to Europe next week.
"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,'' said swim team 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.
"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.''
The AIS said in a statement it was treating the whooping cough outbreak "very seriously'' and would continue to work closely with AIS health professionals and ACT Health to reduce any potential risk.
"We are informing all sports visiting the AIS of the infection and any decision to continue their immediate preparations at the AIS are for each individual sport to make,'' said the AIS.