But he said he had discussed the project during negotiations to form government with the Greens, and it was natural there would be some disagreement.

Greens MLA Amanda Bresnan said her party's opposition to the data centre had no impact on its negotiations with the parties.

''We went to the election with a very definite and strong position on the data centre, Labor and Liberal were both aware of it.''

The Greens and Liberals have said they would not support the development at the Mugga Lane site now proposed.

Its backers, Technical Real Estate, threatened this week to pull the $1billion project out of the ACT if the Government overruled the findings of an probe probe into its environment impacts. Residents in nearby Macarthur say the project is too close to their homes and will produce harmful emissions.

Mr Stanhope said the Greens and Liberals were playing politics and said the planning process should be free of interference.

''We're in the midst of an independent planning process and we have two political parties now saying it should be aborted without allowing the process to run to its conclusion irrespective of what the outcomes of that particular process may be.''

Liberal leader Zed Seselja said TRE's threat to quit Canberra would not alter the party's position on the project.

Ms Bresnan accused Labor of botching the consultation process for the project. But she denied the disagreement over the data centre would set a precedent for unstable government.

''The Greens have always said that we judge each issue and determine each issue on their merits and that's what we will do. It's about making good decisions and considering what's best for the people of Canberra,'' she said.

Mr Stanhope was also unconcerned about disagreements with the Greens.

''The history of minority government is that the government of the day loses a significant number of votes on the floor of the Assembly simply as a result of the operation of minority government and there's nothing to be read into that,'' he said.