The operator of the private clinic, which was set to open in 2020, has warned construction would be postponed again if an agreement to reduce the lease variation charge could not be reached with the ACT Planning and Land Authority next week.

Scheduled to break ground this month, Barwon Investment Partners' planning consultants have warned to expect an additional charge of $1400 per square metre, after varying the size of its dwelling on Crown land.

Stage one of the $22 million Canberra Private Clinic will include more than 3500 square metres and stage two will deliver a further 2600 square metres of floor space.

The Canberra Times understands Barwon is eligible for a 50 per cent reduction in the fees under a coronavirus construction stimulus measure, which it would require to keep the development on track.

Co-located with Calvary John James Memorial Hospital, an existing building would be redeveloped to accommodate the inpatient facility.

The facility will open with 52 beds, 14 dedicated to adolescents and 38 for adults.

Approval has already been granted for the provision of an additional 28 beds in the future.

Outpatient treatment would be provided inside a new building adjacent to the inpatient facility.

In addition to adult and adolescent outpatient rooms, the three-story building would include consultation suites and a carpark.

When the development application was originally lodged for the land, which is directly across from the Royal Australian Mint, Barwon and private hospital operator Healthe Care Australia had proposed for all outpatient facilities to be located in the existing building, meaning fewer beds.

"We decided very early on that the demand would be there to go straight up to the higher amount of rooms," Healthe Care's property manager Mark Sweeney said.

Mr Sweeney said the application of the lease variation charge was flawed as there was no way of knowing what it would be until right at the end of the process.

"We've gone right through planning - DA, detailed design, tender - and we're ready to construct and only now the landlord is finding out what that lease variation cost will be," he said.

Mr Sweeney said they were ready to begin demolition and start building and not being able to was incredibly frustrating.

"We can't get a building approval until the lease variation is resolved and it's only now we've found out how much they intend to charge, which is exorbitant," he said.

Barwon asset manager Mitch Stone said while they were aware a charge would be applicable, indications were the variation would be significantly more than anticipated and potentially prohibitive for the project.

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"Accordingly, we're reluctant to commence construction until this issue is adequately resolved," Mr Stone said.

"We're continuing to work with the relevant planning authorities to resolve this issue so that we can proceed with the delivery of this much-needed facility for the residents of the ACT, southern NSW and the Riverina."

An ACT government spokesperson said the lease variation charge for the development application was yet to be determined by the Commissioner for ACT Revenue.

A determination was expected shortly, the spokesperson said.

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