Canberra Health Services have launched an investigation after junior doctors flagged concerns they were being underpaid.
Staff were told in an email on Thursday colleagues had raised concerns about an issue with public holiday penalty rates, which left some without proper pay.
ACT Network Director of Physician Education Ashwin Swaminathan wrote in the email the issue was being investigated with the external payroll service provider.
"I want to be clear - if any of you have been inadvertently underpaid, you will receive appropriate backpay," he wrote.
"Our external payroll provider is putting in place a new payroll system that will mean the handling of public holiday penalty rates can be automated which will make the process more efficient and accurate."
Liberals health spokeswoman Vicki Dunne called for an independent audit into the health system pay services.
"Hospital staff, especially junior doctors, are tired, sick and burnt out from working double shifts - up to 80 and 90 hours per week - in a highly stressful workplace," she said.
"But, for a junior doctor to claim overtime is onerous, and administratively difficult to process. They know that they are regularly underpaid."
Canberra junior doctors were told via email in March that health services were making changes to reduce unnecessary overtime.
"In particular, we will be looking to make structural changes to the way we conduct our clinical activities so as to reduce the need to stay back late," the email read.
