New health advice was issued on Monday requiring healthcare workers to stay away from work for 14 days once returning from Sydney or Newcastle, due to increasing COVID-19 cases.

Multiple doctors who spoke to The Canberra Times said it could leave the territory with a depleted workforce in the coming months, unless widespread exemptions were granted.

However, the government says it has a detailed workforce plan and no clinical services have been impacted.

Calvary Public Hospital confirmed this week 12 doctors were initially excluded from the workplace, with five of those then given exemptions as essential workers.

However, Sydney doctors were told the exemptions would not be valid for other shifts they had booked in over the coming months, if they left the territory.

One Calvary doctor said the "knee-jerk reaction" meant scores of NSW doctors would be prevented from working in Canberra over the coming weeks and months, with a number of the hospital's departments relying on Sydney locums.

"The hospital has been left with significantly depleted resources," he said.

"In the foreseeable future there will be problems filling those shifts because of this rule."

A spokesman for Calvary Public Hospital said on Friday the hospital was operating as normal with required medical staff coverage.

He confirmed of the five workers who eventually received exemptions, four were emergency department consultants and one was an intensive-care consultant.

Canberra Hospital granted exemptions for all Sydney doctors who worked last week, with many told to take a test and wear a mask while they waited for the results.

However, the widespread exemption policy may not apply for clinicians rostered on in coming weeks and months.

One Canberra Hospital doctor said there seemed to be little communication between the health directorate and the hospital before the new rule came in.

He said the policy could cause staffing chaos across the hospital, with some departments staffed by a significant chunk of Sydney-based locums.

The doctor said it would also see junior doctors stretched, with the Sydney registrars who would usually come to Canberra to cover scheduled leave unable to do so.

"If it can't get sorted for doctors that live in Sydney or ones who need to rotate through Canberra Hospital, then all of our local workers will need to do many, many more hours," he said.

A Canberra Health Services spokeswoman said the hospital would continue to work with all staff about any concerns.

She said the policy was issued in order to keep health care workers and vulnerable people safe from COVID-19, after escalating numbers in Sydney.

"Individual health services can issue exemptions to staff to ensure essential health care is not impacted as a result of this advice," the spokeswoman said.

"All those receiving exemptions have been assessed on an individual basis and are screened daily to minimise risk to health care workers and vulnerable people.

"Canberra Health Services has a detailed workforce plan to ensure our health facilities are well prepared for potential impacts related to COVID-19.

"We are grateful to all of our staff for their ongoing hard work and dedication, as we continue to prioritise the health and safety of our staff and patients."

Australian Medical Association ACT president Antonio Di Dio said the already significant stressors on junior medical staff had been added to by current travel restrictions.

"We would like to support them further and express great appreciation for the amazing work these young doctors continue to do on the front line," he said.