Much of the work will take place during the school holidays and Easter long weekend.

The geotechnical works for the $11 billion Melbourne Metro Rail Tunnel have been completed, laying the groundwork - literally - for construction to begin.

City Square in the CBD will be surrounded by hoarding next month as work proceeds on the tunnel project.

Passengers using the Pakenham, Cranbourne and Craigieburn lines have been warned to allow an additional 40 minutes for their journeys over several days in early April.

Buses will replace trains between Dandenong and Pakenham stations between April 1 and 6 for signalling upgrades to prepare for high capacity trains.

Track maintenance work on the Cranbourne line means passengers will be forced onto replacement buses between Dandenong and Cranbourne stations.

On the Frankston line from the evening of April 7 to 10, buses will replace trains between Moorabbin and Mordialloc stations while track and signalling works are undertaken at the new Southland station.

Most regional train lines will experience long delays in early April. On the Traralgon and Bairnsdale lines, delays of one hour are expected from April 1 to 6 and then again from April 8 to 10.

The Maryborough, Seymour, Geelong and Warrnambool lines will also experience delays throughout next month.

The tram routes on the 8, 12, 78 and 109 lines will also be affected in April.

All routes and delays can be found here.

Ms Allan said the works were being staged so all lines were not affected at once.

She said the "major construction blitz" was being carried out while services were quieter than usual.

Major works will also proceed next month on the Metro Tunnel after 270 boreholes were drilled along the tunnel's alignment to examine ground conditions.

Samples of the rocks collected dated back 440 million years.

Premier Daniel Andrews said the first stage of the project was now finished with major construction work to begin next month.

"This is one of the biggest projects our nation has ever seen," he said.