The ACT Supreme Court has ordered the Heritage Council to drop its decision to heritage list part of the Northbourne Avenue flats precinct.

The ACT Government is planning to demolish the run-down public housing flats as part of its public housing renewal program.

But it has faced some hurdles.

Earlier this year the ACT Heritage Council heritage-listed about 40 per cent of the old flats in the Northbourne precinct.

The council said the flats were an historic example of the post-war international style of architecture.

However, the National Trust wanted the whole precinct to be protected, and took the matter to the ACT Civil and Administrative Tribunal.

Today the Supreme Court ordered the Heritage Council to reverse the partial heritage listing after a clerical error meant the National Trust was prevented from making a submission on the decision.

Eric Martin from the National Trust said the ruling could pave the way for all of the flats to be heritage-listed.

"The National Trust hope that due process will be followed and that the Heritage Council will start the process again and actually provisionally list the whole site," Mr Martin said.

"The National Trust was in good faith advised of a certain date to make a submission, we provided a submission on that date, but unfortunately the date we were advised by the ACT Heritage Council was incorrect.

"It seemed to be a denial of natural justice, which is why we pushed it to the Supreme Court."

But Heritage Council chairman David Flannery said the council intended to re-provisionally register up to 40 per cent of the buildings.

"We're wanting to enter into negotiations with the Land Development Agency as well to see if we can get a moderated position so we can align our decision with what the future holds for that site in terms of development," he said.

"I know the National Trust will want to again appeal any decisions, they're very keen on protecting the whole of the precinct, which is not a position that's getting much support from the community.

"I think there has to be a moderated position on this ... we're trying to pick a middle line here."

Mr Martin said the housing precinct could look better with a fresh coat of paint.

"They were really important in the early stages of Canberra's development from the 1960s, they were the gateway to Canberra, they were designed by a nationally recognised architect, they were of international and national standing as far as the design and they represented some very innovative techniques for the time," he said.

Chief Minister Andrew Barr has previously said the Government would proceed with the development plans, which also affect the proposed light rail project.