More than 10 tonnes of bird poo has been removed from the dome of Melbourne's Flinders Street station as part of restoration works.

The station is undergoing a $100 million makeover, with works expected to be finished by 2019.

Flinders Street station was built in 1910, and this is the first time in more than a century it has had significant cleaning and restoration works.

As part of the project, the building has been periodically covered with scaffolding as it is returned to its original colours.

The clock tower on Elizabeth Street was recently cleaned and restored, and Minister for Major Projects Jacinta Allan said cleaning and restoration on the iconic dome had been finished.

The station was covered with scaffolding for works on its facade. ( ABC Radio Melbourne: Simon Leo Brown )

"The dome really is a symbolic part of Flinders Street station, indeed it could be said that it's the international symbol of Melbourne," she said.

"All up it's estimated there was about 10 tonnes of pigeon poo removed as part of the building works project."

The refuse was treated as hazardous waste and removed from inside the dome by a specialist company.

There is still significant work to be done restoring the old ballroom. ( ABC News: Stephanie Anderson )

Roof repaired in the disused ballroom

The station's neglected ballroom is somewhat legendary among Melbournians, and there have been plenty of proposals for its use, from hosting a craft market to crisis accommodation for the homeless.

The ballroom was in a state of dereliction, and work has been done to waterproof and stabilise its roof.

Ms Allan said no decisions had been made about how the ballroom and other spaces would be used once the works were complete.

"There's certainly been plenty of ideas put forward," she said.

"We also have to make sure that whatever future use is made of this space that it's sympathetic to the passenger movements that come through this station."

Ms Allan said the works were not just about protecting the station's history, but also to improve its useability.

"Flinders Street station is our busiest station – around 200,000 passenger movements go through this station every single week day, 26 million passenger movements a year," she said.