Transport Minister Andrew Constance said the government would try to minimise the length of time the 13.5-kilometre stretch of track would be out of action but conceded that it would "pose a challenge".

"It is going to be a disruptive time – I won't sugar-coat that," he said on Wednesday.

"There will be a period of time where that rail line will be decommissioned and as a result we are going to have to manage the commuter needs through that period."

The time-frame for the temporary closure has yet to be finalised but Mr Constance said it would not be for several years.

The most recent government statistics show more than 25,000 people travel on the Bankstown Line during the morning peak between 6am and 9.30am.

In what he described as a "mega build", Mr Constance announced on Wednesday the start of the tender process to build twin tunnels under Sydney Harbour and the CBD as part of the second stage of the metro rail line between Chatswood and Sydenham.

The first of five giant boring machines are due to start tunnelling by the end of 2018.

Driverless metro trains will begin running on the first stage of Australia's largest commuter rail project between Cudgegong Road station in the city's north-west and Chatswood in 2019. The remainder of the line from Chatswood to Bankstown via the CBD and Sydenham is scheduled to be operational by 2024.

Before the $8.3 billion first stage is completed, thousands of commuters who travel by train on the existing line between Chatswood and Epping will also have to catch buses for about seven months from late 2018 while it is converted to carry metro trains.

The Epping to Chatswood line via Macquarie Park carries about 8000 passengers during the morning peak.

The conversion of the Bankstown Line is one of the bigger challenges facing engineers on the metro project because it involves a major overhaul of the existing rail corridor, which is more than a century old.

Train stations will need to be renovated and tracks and platforms straightened to handle the new trains.

Mr Constance said the conversion was likely to take longer than six months and would "mean changes for commuters during the build of the project".

"We are working through that ... but at the end of the day those commuters are going to get a brand new metro service," he said.

The planning process for the Bankstown to Sydenham line is due to start later this year.

The Transport Minister declined to give an estimate of the final cost of the second stage of the metro project because the tender process had just opened. The preliminary costing of between $9.5 billion and $11 billion released in 2014 did not include the bill for new stations at Barangaroo and Waterloo.

"This is Sydney's super train. We are going to see 45,000 passengers per hour moved on the metro network. This compares to 24,000 on the existing network," he said.

"It is going to be a world-class, single deck, fully automated train."

The government is yet to release a final business case for the second stage of the metro line, or an environmental impact statement.

It is in the midst of acquiring about 150 buildings for the construction of stations along the new line. In Sydney's CBD, 19 buildings – some as high as 22 storeys – face the wrecking ball over the next two years.

Mr Constance said construction of the new line under the CBD was likely to be less disruptive than the $2.1 billion light rail line from Circular Quay to the eastern suburbs because the former was primarily an underground project.

"There will be construction disruption through the heart of the city with the project given the new stops at Barangaroo, Martin Place, Pitt Street, Central," he said.

"[But] you don't have to deal with traffic management as much."