Hundreds of trainee doctors around the country have been left distressed and confused after a complex online exam they were sitting was suddenly aborted due to a computer glitch.

The exam, taken by doctors once they have completed medical training, is a crucial next step for trainees who want to become a physician or paediatrician.

The Royal Australasian College of Physicians, which runs the exam, is investigating the glitch.

Known for its high stress and high stakes, the exam takes the best part of a day to complete, costs almost $2,000 to sit, and doctors can spend 18 months preparing for it.

The system error struck about five hours into the exam, and after several hours of uncertainty doctors were told they would need to re-sit it on March 2.

John Zorbas, chairman of the Australian Medical Association Council of Doctors in Training, said the event caused distress throughout the medical profession.

"This is an exam that some people have studying for years for, and for it to come apart at the last minute because of a technical glitch without a backup system in place is incredibly distressing for these trainees," Dr Zorbas said.

Dr Zorbas said he had been fielding calls from concerned and stressed trainee doctors all day.

"Any trainee who finds themselves in distress, any doctor who is just not coping with the situation should contact the Doctor's Help Advisory Service for support," he said.

"And secondly, we want to reassure these doctors that we're speaking to RACP to find out exactly what's gone wrong and make sure there's an open, fair, transparent system in place."

One person who sat the exam has penned an anonymous letter for fear of professional repercussions if they speak out.

"Candidates were seen outside examination venues crying, distressed, struggling to come to terms with the fact that what was meant to be an evening of relief, was one of more anxiety and uncertainty," the letter reads.

"They have received a 200-word statement from the RACP president that provides few answers about the cause of the failure, and a fairly insincere apology for the serious distress these events have caused candidates."

College will investigate exam bungle

This is the first time the exam was done online and was run by the international IT company Pearson Vue on behalf of the RACP.

Dr Zorbas said the AMA is trying to verify reports trainees raised concerns there was no paper back-up system, and that those concerns were met with silence.

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RACP president Catherine Yelland said the college was also investigating its own handling of the situation.

"We have been in discussions with the examination provider about how this happened, and they will provide a report to us within the next 48 hours," Dr Yelland said.

"We just need to apologise for the distress this has caused, and assure all the members of the college and all our young doctors that we are treating this as the most important issue."

Helen Schultz, a consultant psychiatrist and advocate for doctors in training, said she feared for the mental state of those affected.

"These are doctors who have completed all of their medical training, internship and residency years, and have decided to become physicians," she said.

"So these are really the entry level exams to get very precious training places that the RACP determines."

She said it was an issue she was so concerned about, she would on Thursday open her clinic in Melbourne for emergency appointments.

"They must come if they feel at all unsafe. And if they can't wait until then, they must leave work today and go and see their GPs so that they're safe."