Labor should put tolls on the level crossings they remove and use the money to help pay for projects such as the metro rail tunnel, one of the state's leading transport thinkers says.

The Andrews government has promised to remove 50 level crossings in eight years and Professor John Stanley believes motorists who will benefit from the removal of traffic-choking boom gates should pay a small toll for the time they save.

Daniel Andrews at the Balcombe Road level crossing in Mentone. Credit:Penny Stephens

Speaking this week on a panel organised by Engineers Australia, Professor Stanley of the Institute of Transport and Logistics Studies said the revenue could go into a transport fund that would help the government deliver a long-term plan for Melbourne.

"The general principle is you identify who the beneficiaries are from implementing public policy initiatives and ask them to make a contribution, and the people who are going to benefit from this are the motor vehicle users who get a better run," he later told Fairfax Media.