Trains will return to Melbourne's Frankston Line on Monday after weeks of disruption.

Three level crossings were removed during the longest rail line closure in the city since the construction of the City Loop more than 30 years ago.

The new below-ground McKinnon Station will open tomorrow, with new stations at Ormond and Bentleigh to follow in late August.

Victorian Premier Daniel Andrews said the three level crossings were removed six months ahead of schedule.

"There's been a lot of disruption in recent times. We've had a fleet of about 70 buses running up and down this corridor replacing trains for these last 37 days," he said.

"To every single member of the travelling public, traders, the local community thank you so much for putting up with that short term pain for what is undoubtedly a clear win, clear gain in the long term for this local community and for our state."

Public Transport Minister Jacinta Allan said the State Government was "absolutely determined" to keep up the pace of its level crossing removal project.

"I think tomorrow morning, when the trains start running again, the benefits will be immediately seen through a better train experience, reduced road congestion and, of course, the enormous and important safety benefits that come from getting rid of these dangerous and congested level crossings," she said.

Construction has started on a further 15 crossing removals, which are due to be completed by the end of 2018.