The 18-year-old was diagnosed with supraventricular tachycardia (SVT) before the Rio Games and suffered a sudden attack 20 minutes before the 100m final.
The SVT condition can cause a dramatic spike in heart rate.
Chalmers still appeared keen to race but was pulled from the final by medical staff after consultation with Australian head coach Jacco Verhaeren.
Officials said Chalmers recovered quickly from the episode and was able to walk out unassisted to rejoin his South Australian Institute of Sport team.
Verhaeren expected Chalmers to feature in today’s 200m freestyle in Brisbane.
“It is a condition that we have always been aware of and also of treatment that he has undergone,” he said.
“It is something we knew about in the lead-up to the Olympics and, obviously, we are guided by the doctors.
“It is something that is not a major heart condition but, when it comes, his heart rate escalates quickly.
“We will see how he is tomorrow and he may be able to race – we will have to wait and see.”
Verhaeren said Chalmers was “devastated” about the decision to withdraw from the final of the 100m – the event for which he won gold in Rio.
He had hoped to earn a maiden national title in Brisbane and selection for December’s world short course titles in Windsor, Canada.
There was initial talk of selectors granting Chalmers an exemption but, technically, no 100m spot is available after the top two place getters also clocked qualifying times.
Cam McEvoy defended his 100m short course title in Chalmers’ absence with a personal best 46.19 seconds ahead of Tomasso D’Orsogna.
However, McEvoy is yet to decide whether he will contest the world titles in Canada.
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