The first level-crossing removal has now been completed, with train tracks running under Burke Road. The state government described the crossing at Gardiner Station as among Melbourne's worst.

The new station will reopen on Monday with full train services scheduled to resume.

Premier Daniel Andrews said intensive works had been undertaken to remove one of the most congested level crossings.

"This is one of those uniquely challenging sites where you've got trams, trains and, of course, the road," he said.

The government's commitment to remove 50 level crossings was a central part of its election pitch in 2014.

Mr Andrews said boom gates were down for 40 minutes during peak hour before the crossing was removed at Burke Road.

About 25,000 vehicles move through the crossing each day in addition to 150 trains and 180 trams.

One of the removed boom gates was placed on display beside the crossing and Mr Andrews said it would be shipped off to a museum. "And that's exactly where these boom gates belong. They're relics of the past."

However, a stoush erupted over who should claim credit for the project, with the Coalition saying it had allocated funding for the removal.

Opposition treasurer and Malvern MP Michael O'Brien​ said the removal was a great project but had he hoped for a "bit more honesty" from Mr Andrews.

"This is a project that was entirely funded by the Liberals in the 2014 budget," he said.

It had been designed, funded and put out to tender by the former government, he said.

However, Transport Minister Jacinta Allan said the Andrews government had achieved a level-crossing removal in less than 12 months, which the former government could not manage in four years.

The Burke Road crossing removal is part of a package that includes removing crossings at Ormond, McKinnon and Bentleigh railway stations at a cost of $524 million.

Works are under way at seven level crossing sites across Melbourne.

Ms Allan said more than 30 level crossings would be gone or under construction by 2018.

She thanked retailers for putting up with road closures during the works.