The National Health Co-op chief executive Alison Wright said the clinic would close at the end of July to allow the charity to maintain other services throughout the pandemic.

The organisation had reached out to ACT and federal governments seeking a subsidy to assist the running of the nine other bulk-billing clinics.

"JobKeeper has been a critical component in maintaining services; however, immediate expenses in PPE orders, costs to improve ICT, very little rent relief and intermittent variations in patient attendances have proved a perfect storm for the organisation," Ms Wright said.

Ms Wright said she would meet with the ACT Health Minister on Wednesday to discuss the need for support.

"As a not-for-profit, the challenge for us is sustaining any kind of shock or drop in patient revenue," she said.

At the peak of the pandemic, the 10 Canberra clinics had a 40 per cent drop in patient revenue. After the introduction of Telehealth it was still 20 per cent below normal levels.

"There's still a reluctance from people to really proactively go to their doctor and we want to send a message out that GP clinics are safe to be at."

The future is uncertain for nurses and reception staff at the Charnwood centre.

While doctors would be relocated to Macquarie and allied health workers would go to Higgins, Ms Wright said they were looking at the fate of other staff members.

"We are taking a really significant look at the structure of our nursing and our reception staff and seeing where we can make improvements," she said.

"We've made a commitment to staff to do every thing we can to keep everyone working."

The NHC provide 14 per cent of bulk-billed doctor appointments in the ACT.

Health Minister Rachel Stephen-Smith said the decision to close the centre would be disappointing for patients but it was pleasing the co-op would transfer the clinicians to its other practices in Belconnen.

Asked whether the government would provide financial assistance to the co-op, Ms Stephen-Smith said she would continue to work with all general practice providers.

"We're in a conversation with the national health co-op about how they may be able to work with us to better integrate primary care with acute care across the system and particularly to support those people who are most vulnerable in our community," she said.