Public Transport Minister Terry Mulder says the works would result in a more streamlined and reliable journey for Bendigo passengers and create space to run additional V/Line services in the future.

But Ms Edwards said while the overall project, initiated by the Labor government, would be beneficial, the reality was that there had been a decline in V/Line services since the Coalition formed government. 

"Unfortunately the lack of recent investment has led to significant and consistent delays for commuters as a result of signal and track faults," she said. 

"Commuters face overcrowding every single day and that is set to continue.

"The state government has delayed the ordering of new carriages and even with the regional rail link works, these new carriages won't arrive until post 2016."

She called for much-needed maintenance works on the Bendigo to Melbourne track. 

Federal Member for Bendigo Lisa Chesters said the rail works were great and "not a moment too soon". 

"So many people rely on a fast and efficient train service to Melbourne and it's been frustrating to see services slow down," she said. 

"We need to see the state government speed up the train timetable and get back to those faster services."

Upon completion of the rail link works, the Ballarat and Bendigo trains will progressively begin using the regional platforms at Sunshine and Footscray railway stations and the new V/Line-only tracks between Sunshine and the city.

Mr Mulder said the rail link would deliver more services, more often. 

“The Regional Rail Link project is well under budget and ahead of time and we are on track to commence the new regional services in the first quarter of 2015," he said. 

The Bendigo and Ballarat lines will have a new timetable from July 27.

Buses will replace trains on  both lines from June 28 to July 15.

Member for Bendigo East Jacinta Allan has been contacted for comment.