Calvary has confirmed it will take legal action against the move, which the organisation's national boss has said could put "clinical safety at risk".

Health Minister Rachel Stephen-Smith said the potential court challenge would not stop plans on Wednesday for the Assembly to pass legislation to allow the government to compulsorily acquire the hospital.

"They're going to take legal action, but once the legislation is passed and notified, they will also be legally obliged to work with Canberra Health Services through the transition," she said on ABC Radio Canberra on Wednesday.

A fiery debate is under way in the parliament. Protesters are expected to gather outside the Legislative Assembly.

Some minor amendments will be made to the legislation but it is set to pass with support from Labor and Greens members. The Liberals will oppose the bill.

Calvary had sought to renew negotiations with the government over the future of the Bruce site and said it was forced into legal action as the government did not adjourn debate on the bill.

The government's legislation said Calvary would be paid compensation based on "just terms" but Calvary national chief executive Martin Bowles said he did not believe this was available under the proposed legislation.

"Our review of the proposed legislation and associated regulation indicates that just terms are simply not available and outside of this there is no indication that commercial terms are available to resolve this matter," he said.

"All we have is an announcement and an imposed unrealistic timeline that has distressed our people and could ultimately put clinical safety at risk."

But Ms Stephen-Smith said the government would proceed with its plans to take over the running of the hospital. She said any legal challenge was a separate matter and would be "responded to in parallel with the transition".

Calvary will not provide details of the court action it intends to take, however, an injunction is the most likely option.

The organisation is not able to pursue this until the bill has passed the Assembly.

Ms Stephen-Smith said she was confident the legislation would be able to stand up to any legal challenge. She said she encouraged Calvary to think of the staff at the hospital and to work with the government on the acquisition.

"My message to Calvary's national office team would be to think about the staff and consumers in the ACT and the need to provide certainty and a smooth transition," she said.

MORE CALVARY TAKEOVER NEWS:

The Health Minister will move some small amendments to the bill related to the language used in the bill.

The Canberra Liberals will outright oppose the bill and will not move any amendments. Acting Opposition Leader Jeremy Hanson doubled down on his criticism, describing the bill as "the action of a dictatorial government that is out of control".

"Many Canberrans are rightly appalled by this forced takeover of Calvary Hospital and there is a lot of anger in the community about it," he said.

"The way in which the ACT Labor-Greens government have gone about this is a disgrace and Canberrans should rightly be concerned with how the entire process has played out and the potential ramifications moving forward."

The forced acquisition is the biggest in the history of ACT's self-government and came after negotiations between the government and Little Company of Mary, the organisations that runs Calvary, broke down.

The negotiations were centred around a proposed new hospital for Canberra's north. The government wanted the hospital to be built on the Calvary site.

The government and Calvary could not agree on the time frame of a new agreement. The government wanted a new 25-year agreement with the organisation but Calvary wanted to retain its current contract, which has 76 years remaining.

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