Earlier this month, the state government announced it would fast-track the $11 billion rail project, which involves constructing an underground tunnel through the CBD with five new stations: Domain, CBD South, CBD North, Parkville and Arden.

However, with planning now underway, Mr Andrews is facing growing pressure to reconsider the project's route, which, unlike the former Napthine Government's preferred alignment, no longer includes additional platform upgrades at South Yarra Station – a key interchange for users of the Dandenong, Frankston, Cranbourne and Pakenham lines.

Commuter groups and council officials have hit out at the decision, saying that South Yarra Station was already stretched, and would only worsen without the necessary infrastructure.

Stonnington Mayor Melina Sehr said part of that growth would come from the development of over 3000 new dwellings in an area next to the station bound by Toorak Road and Chapel Street known as the Forrest Hill Precinct – the kind of urban growth that successive governments had actively encouraged.

"So we would have expected that as part of the Metro rail program, at the absolute minimum, there'd be a significant upgrade to the train station to accommodate that growth," she said.

"It appears that, while the Melbourne Metro rail project is a wonderful project, they've just glossed over South Yarra train station. It just defies logic, to be honest."

The latest publicly available data on station patronage, dating to 2011-12, suggests that South Yarra is one of Melbourne's busiest stations, with 8344 entries on any given weekday, including 2268 during the morning peak.

However, the station has not had a proper upgrade in decades, and commuters are often forced to wait in long queues during the afternoon peak to touch off their myki passes before they can exit.

Public Transport Users Association spokesman Daniel Bowen said the government should examine if it was feasible for the Metro Rail project to include an interchange at South Yarra given the station was already under pressure.

He added: "An additional concourse and entrance onto Yarra Street should be considered to help relieve the crowding and provide a quicker way to and from the station for passengers from Melbourne High School and nearby residents and workers, including those who walk north from the station across the river into Cremorne."

The Sunday Age understands that the government's new Melbourne Metro Rail Authority is expected to talk to the council as planning takes place, but a new underground interchange at South Yarra is not in the current scope of the project.

Public Transport Minister Jacinta Allan said the project would nonetheless cater for growth in the area, and across the city more broadly, by creating extra capacity across the system.

"Melbourne Metro allows 20,000 extra people to use our train network in peak hour. Unless we build Melbourne Metro, people in South Yarra and across Melbourne will be stranded on a crowded, unpredictable train network," she said.

Opposition public transport spokesman David Hodgett disagreed. "Daniel Andrews clearly has not thought this through," he said. "Labor's rail tunnel alignment does not deal with the capacity issues at South Yarra. Under Labor's plan, commuter congestion will worsen."

Construction of the tunnel is due to start in 2018, and be completed by 2026. It is yet to be fully funded.