The accusation comes as new figures show charges relating to driving on toll roads have continued to place an enormous burden on the Magistrates Court.

Of all types of charges, those for driving on CityLink without a valid pass topped the list in the Magistrates Court for 2015-16, increasing 25 per cent on the previous year to more than 45,830.

The equivalent charge for EastLink rose by a massive 52 per cent to 27,300 in the same period.

The combined number of charges for CityLink and EastLink was more than double the second most common charge in the court - theft, on almost 34,000.

The Magistrates Court's 2015-16 annual report was tabled in State Parliament last week. It is understood figures for 2016-17 show that although the number of toll road charges dropped substantially, CityLink still accounted for the greatest number of charges in the Magistrates Court.

When motorists fail to pay their tolls, Transurban hands the matter over to the Justice Department. The case can end up in the Magistrates Court.

Costs to motorists mount rapidly after the department takes on the infringements, but Transurban's invoice fees also account for a substantial part of the overall debt.

In July this year, the company increased its invoice fees in Victoria to $12.39 for a first toll invoice and $24.48 for a second and final invoice, in addition to the initial cost of travelling on the toll road. Those fees are imposed on top of toll travel amounts that can be as little as $1.51.

The CityLink invoice fees are applied for bills that cover up to three days of travel.

Denis Nelthorpe, chief executive of WEstjustice, which provides free legal help in Melbourne's west, said a toll invoice with administrative fees exceeding the actual cost of using the road was often the first contact a motorist received from the company.

"CityLink's rapid toll fee increases are excessive and in our experience discourage customers from paying, which can lead to people getting trapped in the infringements system," he said. "Toll invoice fees should only seek to recoup actual expenses incurred, not punish customers simply for being late or not having an e-tag."

He said Transurban had tried to improve hardship processes, but that would have limited benefits if fees and charges remained unfair.

EastLink charges $5.53 per first invoice, which can also cover up to three days of consecutive travel on the tollway, in addition to a fee incurred from VicRoads that is less than $3. EastLink's invoice fee doubles for a second notice.

A Transurban spokeswoman said more than 95 per cent of customers paid their tolls on time and avoided administration fees.

"We do not profit from fees," she said. "There are large costs involved in collecting unpaid tolls, including the specialist roadside equipment and technology as well as numerous systems, processes and back-office functions."

The spokeswoman said the company did all it could to settle unpaid tolls before they reached the infringement stage, including up to 10 attempts to make contact via phone, text message and email.

The Age has spoken to multiple people caught up in the infringements system, including one woman who racked up $80,000 in CityLink fines.

The woman said she feared going to her letterbox and finding dozens of fine notices. After appearing in court, the total debt was reduced to less than $2000.

Transurban is preparing to build the $5.5 billion West Gate Tunnel project, which will provide an alternative to the West Gate Bridge. As part of that deal with the Andrews government, it has sought to extend its toll deal on CityLink by up to 12 years.

Opposition spokesman Ryan Smith said the government was cosying up with Transurban, which had a "long history of gouging excessive payments" from motorists.

"Transurban's cost recovery regime far exceeds that of its competitors, which should make Victorians very sceptical about whether this $5.5 billion project represents anything near good value for money," he said.

A government spokesman said the system to manage CityLink toll infringements was established in 1999 and talks were under way with Transurban to make it fairer.

He said the government was appointing more magistrates and overhauling the state's infringement system to help Victorians manage their fines.

Financial and Consumer Rights Council executive officer Sandy Ross said high invoice fees charged by Transurban had a "destructive effect" on many motorists.

"They put pressure on people for relatively small amounts of original debt that can trigger larger problems," he said.

Victoria Legal Aid acting managing director Cameron Hume called for better debt management from Transurban and urged it to use its influence to separate the enforcement system from the criminal courts.

A spokesperson for Toll Redress, which is lobbying to reform the system, said some people were being charged as much as $30,000 for a few thousand in unpaid tolls.

"We question whether Transurban are being transparent when they say admin fees are their actual cost," the spokesperson said.