Up to six critically endangered golden sun moth populations could be affected by the second stage of light rail, government documents reveal.
The potential destruction of the moth's habitat is one of a number of environmental and heritage concerns to be considered by the federal Environment Minister.
The Environment Protection and Biodiversity Conservation referral documents were made available on Tuesday and are now open for public comment.
The government submitted two light rail referrals for stage two of the project: one for the route from Alinga street to Commonwealth Park, and the other from Commonwealth Park to Woden, via the Commonwealth Bridge and State Circle.
The government decided to split the approval process in two, anticipating the process to be more complex from Commonwealth Park to Woden largely due to the national heritage implications.
That stage will need the environment minister's approval and to pass through Federal Parliament.
The project will most likely need to run wire free in parts, including through Civic, across the Commonwealth Bridge and through the Parliamentary Zone.
An expansion of the Mitchell depot has been flagged and at least 16 extra light rail vehicles would be needed to service the extension.
If the minister decides the environmental and heritage concerns are likely to have a significant impact, the project will require specific approvals under the EPBC Act - known as a controlled actions.
The presence of golden sun moth along both routes is one of the concerns to be considered.
She will also consider whether both projects - but predominately the second stage - will have a significant impact on national heritage listed places and on Commonwealth land prices.
These heritage considerations include the York Tree Plantation, State Circle cutting, Parliament House, The Lodge and Old Parliament House.
The government will consider having grassed track slab surface treatments around sensitive areas, such as the main avenue approaching Parliament House, to lessen the light rail's visual impact.
The government gave a worst case scenario that more than six hectares of the moth's habitat across both projects could be lost.
It will get an independent environmental auditor to assess the delivery of the project.
The documents said the government decided on the rail route via the western side of Commonwealth Avenue to best serve city west, West Basin and the Australian National University.
It said the eastern side would be better serviced by an east-west link of the light rail network, as part of a potential future route from Belconnen to Russell and the airport.
"Failure to traverse the western side of London Circuit as part of the project corridor means that it would be unlikely for the western side of London Circuit to ever be served by light rail," it read.
The documents note the ongoing uncertainty over the design for the new bridge to be built between the existing Commonwealth Avenue road bridges.
The documents say the project will require four extra road bridges.
One would be built in between the existing Commonwealth Avenue road bridge over Lake Burley Griffin, a new bridge crossing Flynn Drive, a new Adelaide Avenue bridge over State Circle and a new Adelaide Avenue bridge over Hopetoun Circuit.
Transport Minister Chris Steel said he hoped the federal government agreed to the proposal to split light rail stage two into two parts.
"This will provide an opportunity to fast-track the first stage from the City to Commonwealth Park while we continue to work through the more complex later stage through the parliamentary triangle with the federal government," he said.