An artist's impression of the Melbourne Metro rail project's Parkville station. Construction of the $11 billion rail tunnel will create major traffic disruption and will hurt existing businesses during its nine-year construction phase. Flinders Street will be closed to traffic for six to 12 weeks, between Elizabeth and Swanston streets, while a below ground walkway is built between Flinders Street station and the new CBD South station. About 30,000 cars a day will have to be diverted. There will also be environmental impacts. Almost 800 trees, many of them mature, will be cut down for the twin nine-kilometre rail tunnels, Mr Wynne said.

Responding to an Environment Effects Statement compiled over seven weeks, the government has made several changes to the tunnel's design. These include cutting the number of property acquisitions at the tunnel's western entrance in Kensington from 22 properties to just one home, by extending the length of the tunnel entrance. This will involve building a rail bridge over Kensington Road, an option the MMRA had previously said would increase the project's cost. On Wednesday, the authority's acting chief executive Peter Wilkinson said the longer tunnel entrance would not add significant cost to the project. Other changes the government confirmed include tunnelling beneath CityLink's Domain and Burnley tunnels instead of above them, which will remove the need to destroy about 100 trees, and lowering the new CBD South station between Flinders Street and Collins Street by four metres.

The government has also abandoned its plan to use Fawkner Park in South Yarra as launch site for one of two massive tunnel boring machines, and to build permanent emergency access shafts in Fawkner Park and Domain parklands. The state opposition and the Greens both argued the expert panel's finding that a South Yarra interchange might be needed one day should prompt a rethink by the Andrews government, which has rejected the interchange because of its estimated price tag of almost $1 billion. "South Yarra station is Melbourne's busiest outside of the CBD and will only continue to grow in coming decades," Opposition public transport spokesman David Hodgett said. "There is simply no rational reason to have this new rail line come within 100 metres of the South Yarra station and not have an interchange." Greens MP for Prahran Sam Hibbins said the government should "go further" than the panel's recommendation and build the interchange as part of the project. The finalisation of the EES means the government can start constructing the tunnel.

The Melbourne Metro project will run under Swanston Street, build five new railway stations, give three of Melbourne's busiest lines their own tunnel through the CBD, relieve pressure on the City Loop and connect Parkville and Domain to the rail network. The government has conceded that, over its nine-year construction timeline, there will be a big loss of public and private car parking, and that the large construction workforce building the tunnel will generate a high amount of local traffic. "During construction, road closures and restrictions will give rise to increased traffic congestion and delays in and around precincts," Mr Wynne said. Traffic issues would be most severe in Grattan Street, Carlton, and on Domain Road in South Yarra, as well as along St Kilda Road and Flinders Street. Bus services to Melbourne University and the No.8 tram through South Yarra will also have to be re-routed for the project. The project, Mr Wynne has said in his response, "will generate considerable disruption and inconvenience" on residents, creating "stress and anxiety" for many "due to the uncertainty of the design or extent of impacts, such as noise and vibration".

Those affected will have the benefit of a new railway line when it is completed, he wrote, but needed to be carefully considered during its construction. Access to the new Parkville station – next to the new Victorian Comprehensive Cancer Centre and the Royal Melbourne Hospital – may also change, at the request of Melbourne Health. Earlier plans included a station entrance on the southern side of Grattan Street. But Mr Wynne accepted a request from Melbourne Health to put the entrance on the northern side of Grattan Street, outside Royal Melbourne Hospital, instead.