The 18-year-old swimmer has Supraventricular Tachycardia (SVT) which occasionally causes his heart to race.
Chalmers, 18, has Supraventricular Tachycardia (SVT) which occasionally causes his heart to race, but he hadn't had an episode this year until just before Thursday evening's 100-metre freestyle final in Brisbane.
He was examined by medical staff and advised not to swim.
Chalmers, the surprise 100m gold medallist in Brazil, had surgery last year in an effort to improve the condition and it is likely he will need further treatment at some point in the future.
"I'll be training and then my heart rate will just randomly go up and sit at 200-plus for half an hour," Chalmers said earlier this year.
"I can feel it, it makes me go all dizzy."
The condition has not prevented Chalmers from racing at other national trials or major championships in the past two years.
National head coach Jacco Verhaeren said Chalmers' heart-rate settled down before his most recent final and he still wanted to race but was convinced it was not worth the risk.
"He was devastated because he's never been national champion and he wants to make the team," Verhaeren said.
"But there's nothing more important than his health and he gets it."
In Chalmers' absence, Cameron McEvoy successfully defended his national title, setting a personal best time of 46.19 seconds.
Verhaeren said the selectors would meet Friday to discuss the situation with Chalmers regarding the world short course championships.
"It's really to what extent the rules allow us to make an exception," he said.
"It would be unfair also to the ones who raced to say: 'No, we're putting him on', but I'm sure we're going to have a busy meeting."
Verhaeren said Chalmers might still be able to swim in Friday's 200m freestyle and qualify for the December world championships in Windsor, Canada.