A permit application to chop down 77 trees along the leafy boulevard between Dorcas Street and Kings Way, including a section of the Albert Road Reserve, has been lodged with Heritage Victoria by the consortium building the $11 billion Melbourne Metro Tunnel.

Heritage Victoria will make a decision within 60 days.

The tree removals, required for the new underground rail project, would see the largest number of trees cut down along the boulevard so far - possibly in one fell swoop - with experts warning this would seriously tarnish St Kilda Road for years even after new trees are planted.

It comes as the Andrews government announced it has signed a $6 billion contract to build the nine kilometre tunnels and five underground stations with the Cross Yarra Partnership consortium led by Lendlease, and a $1.1 billion contract for high-capacity signalling with CPB Contractors and Bombardier Transportation.

Draft plans for the new Anzac Station detail a significant transformation of St Kilda Road, and have stirred controversy over an new design for bike lanes along the boulevard, and the decision to push ahead with the massive removal of trees.

The Melbourne Metro Rail Authority has promised to plant an extra two trees for every one removed, and suggests that they would be planted in improved soil conditions and with better irrigation.

But arborist Dr Gregory Moore, the chair of the National Trust of Victoria's Register of Significant Trees, said the new trees to be grown off-site would be five metres tall, and would take "considerable time" to have the same impact of the mature trees.

"They are really good elms and in an important heritage precinct for Melbourne ... people will certainly realise the landscape around that area will be significantly different from what it is today."

"Their removal is being done without proper thought or consideration of the value of those trees, the shade they provide, and the impact of the Urban Heat Island Effect."

The Authority plans to chop 95 trees along St Kilda Road (down from 170) and a further 198 trees are set for removal around the new Parkville Station.

The total number of trees to go is 770, which was reduced from 900, following a vocal campaign opposing the tree felling.

Liberal Member for the Southern Metropolitan Region Margaret Fitzherbert accused the government of burying plans for tree removals in site maps.

"Locals have been continually drip fed information about the project," she said.

The Authority's plan for Domain Station has been further criticised for favouring a "Copenhagen-style" bike lane along St Kilda Road, which would see the lanes run along the left-hand side of the boulevard - an option that has been deemed less safe by VicRoads.

VicRoads wants to see two central car lanes removed to make way for a new bike route, which is an approach backed by Port Phillip Council and the Bicycle Network.

The car lanes would be moved to the side, so that the centre of St Kilda Road would become a safety zone for bikes, from Linlithgow Avenue near the National Gallery of Victoria to just north of St Kilda Junction.

Bicycle Network's chief executive Craig Richards said the Authority's plan was found to be unsafe because of the high number of driveways that cut across the path of bike riders.

"We need to stop it. Separated bike lanes in the middle of St Kilda Road will be safer and easier for everyone," he said.

"The plan for lanes down the side of the road was ruled out because it was unsafe for riders and difficult for cars needing to access driveways."

Between 2011 and 2016 a total of 122 cyclists were reported as injured on St Kilda Road - the highest rate of reported crashes involving car doors and cyclists in the state.