Victorian transport authorities have drawn up secret plans to build a second Metro Tunnel, and divert the Frankston Line out of Flinders Street and Southern Cross stations.

The leaked blueprint for the state's rail system also details plans to extend Metro services to Melton, Wyndham Vale and Wallan.

Plans for a second Metro Tunnel have been unveiled. (9NEWS)

Transport for Victoria’s “Victorian Rail Plan” was completed in August, and outlines various stages of planned network enhancement.

Melbourne Metro Two would be built in two stages, and connect the Werribee Line with the Mernda line via Fishermans Bend, Southern Cross Parkville and Fitzroy.

The politically sensitive Frankston line would be re-routed out of the city’s two busiest stations (Flinders Street and Southern Cross), but run via a reconfigured City Loop to Craigieburn.

The leaked blueprint. (9NEWS)

“Melbourne Metro Day One” (currently scheduled for 2025)

- Metro Tunnel 1 from Kensington to South Yarra

- Cranbourne line duplication (from Dandenong to Cranbourne)

- Somerton Link (connecting Upfield Line to Cranbourne and Seymour lines)

- Hurstbridge Line upgrade stage 2 (between Greensborough and Eltham)

“Stage 3”

- Melbourne Airport Rail Link (via Sunshine to Southern Cross)

- City Loop Reconfiguration (Frankston Line to run via Parliament, Melbourne Central, Flagstaff and West Melbourne to Craigieburn)

- Burnley Junction Rationalisation (Glen Waverley line to run via Flinders Street and Southern Cross to Upfield)

- Melton Electrification (construction of extra tracks between Sunshine and Melton)

- Wyndham Vale Electrification (construction of extra tracks between Sunshine and Wyndham Vale)

- Waurn Ponds duplication (between South Geelong and Waurn Ponds)

- Clyde Extension (Cranbourne line extended to Clyde)

- Baxter Electrification (Baxter line extended to Baxter)

- Mooroolbark to Lilydale Duplication

“Stage 4”

- Melbourne Metro 2 West (Tunnel from Newport to Parkville via Fishermans Bend and Southern Cross)

- Laverton and Williamstown Line Upgrade

- Wyndham Vale to Black Forest Road extension (connecting Wyndham Vale line to Werribee)

- Track quadruplication Sunshine to Watergardens

- Wallan Electrification (extension of Upfield Line to Wallan)

- Bendigo Track Upgrade

- Shepparton Line Upgrade Stage 2

“Stage 5”

- Melbourne Metro 2 East (Tunnel from Parkville to Clifton Hill via Carlton and Fitzroy)

- Wollert Extension (Spur off Mernda Line from Lalor)

- Geelong Electrification

- Regional Rail Link Additional Stations

- Barwon South West Line Intercity Upgrade

- Gippsland Line Intercity Upgrade

- Loddon Mallee Intercity Upgrade

“Stage 6”

- Track Pair- South Yarra Portal to Caulfield (extra tracks)

- Track Pair- Caulfield to Huntingdale via Chadstone

- Rowville Extension (via Monash)

- Track Quadruplication Huntingdale to Dandenong (extra tracks)

- Track Quadruplication Deer Park to Melton (extra tracks)

- Track Duplication Bacchus Marsh to Ballarat (extra tracks)

- Track Pair Flinders Street to Southern Cross (extra tracks)

But missing from the plan is Labor’s flagship “Suburban Rail Loop”, which was developed in secret.

Opposition Transport Spokesman David Davis accused the government of a cobbled together transport plan.

“They’re now making it up as they go,” he said.

A government spokesperson said Transport for Victoria conducts a range of modelling.

“This is an internal working document and not government policy”, she said

“Government policy includes removing 50 level crossings, the Suburban Rail Loop, the Airport Rail Link and the Western Rail Plan – projects that will get Victorians where they need to go.”

Metro Two would be built in two stages. (9NEWS)

It comes after Labor unveiled its plans to bring high speed rail to Geelong.

Premier Daniel Andrews committed $100 million for planning to add extra tracks and extend Metro services to Melton and Wyndham Vale, paving the way for faster regional trains.

But he’s promised a more conservative project than Opposition Leader Matthew Guy, who earlier this month pledged to have trains running between Melbourne and Geelong in 32 minutes, within four years.

Mr Andrews said the project would take a decade to complete.

Premier Daniel Andrews said the project would take a decade to complete. (9NEWS)

“Thirty-five minutes would be what you’d be aiming for,” he said.

“But you’ve got to get the order right, you’ve got to get the planning done”.

“Anyone trying to convince people that you can have trains running at 200 plus km/hr sharing the same track with metro suburban trains in the west of Melbourne is trying to con Victoria”.

But Shadow Treasurer Michael O’Brien attacked the Premier’s stance.

“This is a panicked response because he doesn’t have any plan to build fast rail in the next four years.”

More to come...