Toll road operator Transurban says it will cut some of its fees, amid controversy over the millions of dollars it rakes in from customers on top of the charges it issues for using its roads.

Leaked documents seen by the ABC showed in 2016 the toll road operator collected $153.4 million in fees from its customers using toll roads across Australia.

Nearly $54 million of that came from Melbourne's CityLink road users.

Separate to tolls paid for using the roads, motorists are charged fees for e-tag devices, for having bills sent to them and for matching licence plates to CityLink accounts.

The documents show an e-tag costs the company just $10, but users are charged $55.

Transurban has rejected claims it lacks transparency. ( Transurban )

Transurban's Victorian group executive, Wes Ballantine, told ABC Radio Melbourne the actual price of a single e-tag unit did not reflect the costs.

"There's a whole range of charges that are incurred in regard providing that tag, the processes that go on behind it and the technology there to produce it," he said.

"Without the back office system that allows that tag to be used it's just a piece of plastic."

The internal document recommended reducing the e-tag charge to just $15, but the CityLink website still lists the fee as $55.

Transurban charges should be reviewed, advocate says

Denis Nelthorpe from community legal centre West Justice Connect said the company was not operating with enough transparency.

"Electricity companies are subject to price scrutiny, gas companies are subject to price scrutiny, if you use a taxi on the toll road its fares are subject to pricing scrutiny, but Transurban is not," he said.

"It is time that both the major parties accepted that if they are going to have toll infrastructure built into the economy … the appropriate measure is to have these tolling companies and their pricing regimes subjected to the scrutiny of the Essential Services Commission."

The Essential Services Commission is an independent regulator that advocates for Victorian consumers.

Mr Ballantine rejected suggestions Transurban lacked transparency and oversight in setting its fees.

"To say that there's no scrutiny on our prices and fees is just abjectly incorrect," he said.

He said the company would be announcing reductions in some fees next week.

The Victorian Government is extending tolling on CityLink by more than a decade to pay for its Westgate Tunnel road project.

Acting Premier James Merlino said enforcing the conditions of fees in Transurban's contract was a matter for VicRoads.