The Barr government released its preferred route for the second stage of light rail on Thursday, scotching the Parliament House option in favour of snaking through Barton and Parkes on the way to Woden.

But because the rail line will run over Commonwealth land, the NCA can scuttle the route if they chose.

The National Capital Authority's chief executive Sally Barnes said the authority did not support the territory government's plan to reduce traffic from six to four lanes along Commonwealth Avenue and the bridge, and add an extra set of traffic lights.

She said reducing road capacity when the population of Canberra was growing would "negatively impact on traffic movements over the long term".

"The proposal is the most significant change to the Central National Area, and in particular the National Triangle, since the 1974 decision to locate Parliament House on Capital Hill," Ms Barnes said.

"A project of this magnitude requires careful consideration of all the impacts to the heart of Canberra."

She said the NCA had reminded the government of their preference for no overhead wires in the Parliamentary Zone, as well as the need for an appropriate standard of landscaping, urban design and infrastructure.

Ms Barnes said she was also worried about plans to reduce car parking in Barton, and has asked for assurances there will continue to be parking along the route.

“The proposed light rail route highlights the important role the NCA serves to safeguard this area of national significance for future generations of Australians," Ms Barnes said.

"We need to carefully consider the associated impacts of the proposed works as well as clearly identify the benefits of this new transport route for Canberra."

Transport Minister Meegan Fitzharris said the government was considering building a new bridge in between the existing Commonwealth Bridge for the light rail.

"It’s a really important part of this route – not only for city to Woden, but for the whole city – to get over Lake Burley Griffin," Ms Fitzharris said.

"Simply there are two options. One is to be on the existing road surface, the other is to build a new bridge in the middle of the existing bridges.

"Recently the NCA had some public consultation and put forward their proposal that Commonwealth Avenue be reduced to two lanes of traffic. They have not settled on that view. They have now asked us to consider light rail on a new bridge in the middle of Commonwealth Avenue bridge. And that’s the work that we are doing now."

Engineers Australia's Rolfe Hartley said Commonwealth Bridge presented no "insurmountable" engineering challenges.

"Commonwealth Avenue bridge is actually quite strong and certainly capable of taking a light rail system as is pretty much, although it might need additional reinforcing, but by the nature of the bridge it could do it," Mr Hartley said.

"It's a box girder so it's hollow inside. It's essentially a big strong concrete box. Kings Avenue bridge is different, it's narrower, with two lanes instead of three, and made of reinforced concrete. The third bridge is always an option, but it comes down to the planners' design."

Asked about the traffic impact of building light rail on existing lanes, Mr Hartley said it was an issue traffic engineers could overcome.

"Some years ago some necessary expansion joints on Commonwealth Bridge had to be replaced and that meant closing one carriageway for a period of time and making it a single carriageway bridge. There weren't that many traffic problems," Mr Hartley said.

"All of the technical challenges of sending light rail over that bridge into the Parliamentary Zone can be solved."

Like with stage one of the light rail, the ACT government will have to file a formal works approval with the NCA. The NCA will then put the project out for public consultation, the results of which will determine their decision.

Stage two will also have to be rubber-stamped by the federal parliament. ACT Liberal Senator Zed Seselja has already indicated he will try to refer the proposal to an inquiry for an extra layer of scrutiny.

Ms Fitzharris said she "continued to be worried about what the Canberra Liberals will do to undermine this project".