More than a dozen homes and a CBD apartment building will make way for the new Melbourne Metro rail tunnel, after the Victorian Government announced the number of property acquisitions for the project.

Melbourne Metro Rail Authority started notifying property-owners and tenants along the nine-kilometre route on Monday night.

Nine homes in Kensington, five in South Yarra and a city building with 49 apartments are on the list.

Two commercial buildings in Parkville, 14 in the CBD and 13 in Kensington will also be acquired, with a total 94 titles to be affected between South Kensington and South Yarra.

Public Transport Minister Jacinta Allan said the acquisitions were mostly around stations and tunnel entrances.

"Around the points at which the tunnel is diving underground at either end, that's where the acquisitions are primarily concentrated," she said.

Ms Allan said the homes and businesses would not be formally acquired until planning approvals were granted, which was likely to be in 2017.

She said it was a "difficult but necessary process".

"This is a difficult process, particularly for those people who have been contacted over the past few hours, [who've] been notified that their property is required for this project," she said.

"A lot of work has gone in by the authority to ensure that people are treated with respect and fairly."

Acquisitions just the 'tip of the iceberg'

But Victorian Opposition Leader Matthew Guy criticised the rail authority for leaving notes on people's doorsteps.

He said the State Government had failed to explain how it would fund the entire project, release a business case, or complete an environment effects statement.

"If this Government can't tell Victorians how the project is going to be funded, yet they can scuttle around and tell people they have to leave their home, then this is a substandard way of building infrastructure," he said.

Mr Guy predicted many more properties would have to go to make way for the tunnel.

"The hundred or so that have been announced in terms of overall numbers today I suspect is just the tip of the iceberg," he said.

"[Premier] Daniel Andrews and Jacinta Allan know that and they're not telling the truth by telling Victorians that this is the final number that are going to be acquired."

Greens Melbourne MP Ellen Sandell said residents whose properties were to be acquired should be consulted meaningfully and compensated fairly.

"The Government must learn from the mistakes of the failed East-West toll road and make sure residents are properly informed and compensated for the loss of their homes," she said.

"We need to see the money on the table and more detail to make sure this isn't just about managing the PR, like we see in the TV show Utopia."

The Government said it was too early to say how much the property acquisitions would cost, but there was $4.5 billion in funds already available to progress to this stage.

VicTrack and council land will also be used.

Business owners given two years to vacate

Max Stern said he set up his stamp and coin shop in the Port Phillip Arcade nearly 60 years ago.

Max Stern's business will be acquired to make way for the Melbourne Metro. ( ABC News: Margaret Paul )

"I started with one shop during the Olympics in 1956," he said.

He received a letter on Monday morning from the Melbourne Metro Rail Authority to say his business would likely have to make way for the project.

"I rang the agent, he didn't know, I rang the owner, he didn't know - it just came out of the blue," he said.

"Shock and disbelief - I just had to read it twice before I could realise what was going on."

He said he was not interested in compensation.

"I'm not after the money, I want to stay here because we are an icon in the city."

Millon De Kauwe said his restaurant in the Port Phillip Arcade in the CBD would be acquired but he had not been told whether he would be compensated.

Mr De Kauwe, who has owned Jolly J's for 15 years, said other shop owners received minimal information.

"[I was told] last evening, maybe around 6.30pm, 7:00pm," he said.

"When they came in I was quite busy with customers and I couldn't talk to them but they just left me a leaflet, and like my shops next door they were saying we've got to vacate in two years time."

Hundreds of people have previously been warned their properties will need to go to make way for the $11 billion project, which will feature five new underground train stations at Arden, Parkville, CBD North, CBD South and Domain.

The Melbourne Metro Rail Authority also sent letters to more than 20,000 people who may be affected by noise and infrastructure changes.

The Government has yet to put a price on the acquisitions, but the Greens had argued property owners should receive more than fair market value for their land.

Construction for the project is scheduled to begin in 2018.