A junior doctor at Canberra Hospital earlier this year raised the alarm about the pay discrepancies and presented a report on her findings to Canberra Health Services.

She believed the issues were systemic.

The hospital has acknowledged there may be problems with the doctors' pay, stemming from a lack of consistency on how pay entitlements are processed.

Internal ministerial briefings, released under freedom of information, said Canberra Health Services was expecting to receive details from the Australian Medical Association with details of those who thought they had been affected.

"Instead a letter was received from Hall-Payne Lawyers who are now representing 63 junior medical officer staff who believe they have been paid incorrectly," the briefing notes said.

The law firm has provided the government with a statement of claim.

"The matter is currently being evaluated and Canberra Health Services has sought the assistance of the ACT Government Solicitors office to help in responding to the matters raised and provide advice to CHS," the ministerial briefing said.

"This matter cannot be finalised until an audit is conducted to determine exactly what the issues are, the extent of any overpayments and/or underpayments and how the matters may be settled to all the parties' satisfaction."

Some doctors have been pushing for an independent audit of their pay, however the hospital has been investigating ways to undertake a sample of cases.

"If a full audit were to be undertaken of all [junior doctor] payments this would be a time intensive and resource intensive exercise as the [junior doctors] are paid off manual timesheets," the briefings said.

"It is not easy to shorten the amount of time that such an audit would require as it would need to be undertaken by staff who have a payroll background and understand the nature of these payments and can read and interpret the timesheets accurately."

A Canberra Health Services spokeswoman said internal investigations had revealed the majority of issues related to public holiday pay.

Payroll has developed an excel-based automated tool to assess the accuracy of public holiday payments to affected staff over recent years.

"This is expected to resolve the issue of backpay for most [junior doctors], with unresolved issues to be addressed on a case-by-case basis," the spokeswoman said.

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"Given the capacity to implement an automated solution, a full audit is not considered to be the most effective way to resolve the issue for the junior medical officers involved.

"We understand that the [junior doctor] representative group is pleased with the progress to date and the active engagement from Canberra Health Services to have their issues addressed.

"This engagement will continue, recognising the importance of supporting junior doctors and ensuring that enterprise agreement entitlements are correctly applied."

The spokeswoman said a fully automated pay system in development would ensure the errors did not happen in the future.

She said productive meeting had been held with junior doctor representatives including the Australian Medical Association and the doctors' union.

It comes amid concerning stories about workplace bullying, harassment and unsafe working hours Canberra's junior doctors have been working.

An internal review of physician trainees' conditions said doctors were working excessive hours in breach of their enterprise agreement.

It was leading to high fail rates and burnout among the cohort.

The report said doctors were pressured not to take sick leave, told the system could not deal with them taking time off.

Earlier in the year, a report Medical Board of Australia found ACT's junior doctors were facing the highest rates of bullying in the country.