Toll company Linkt says tens of thousands of Victorian motorists may have been incorrectly charged after travelling on CityLink and the West Gate Tunnel.

Transurban, the company who run Linkt, apologised to customers on its website and said it was now re-examining a decade of charges to rectify mistakes.

“Customers have got a reasonable expectation we get the bill right every time, and in this instance we’ve really let people down,” Transurban spokesperson Chris Jackson told 774 ABC Melbourne radio.

An estimated 1.4 million trips on the toll roads are believed to be affected by the error.

A car drives along CityLink in Melbourne's inner west.

Errors which lead to incorrect charges could stretch back a decade according to parent company Transurban. (Supplied: Transurban)

Mr Jackson said the issue had been traced to Linkt’s systems incorrectly identifying the classification of vehicles, where different sized vehicles are charged different amounts.

“We’ve identified about 90,000 vehicles that have been incorrectly classified to some degree,” he said.

“To put this sort of matter into context, this issue impacts less than 1 per cent of trips.”

Mr Jackson said the company would both be issuing full refunds adjusted for inflation, and providing a compensation payment for affected drivers.

“Customers don’t need to do anything. We’ll be in contact with them if they have been overcharged,” he said.

“We will also be making an additional payment to customers to recognise the significant inconvenience that this has clearly caused.”

The green Linkt sign on a CBD building.

Linkt says it will directly contact any motorists affected by the issue to provide refunds. (ABC News: Christopher Gillette)

Drivers who may have been undercharged their tolls as a result of the mistake will not be required to pay back the difference.

The company said on its website it would improve its classification processes to improve accuracy and prevent future issues.

The mistake comes a year after Transurban was forced to apologise to Canberra drivers after admitting some motorists were charged for trips that were never taken.

Linkt asks any drivers who believe their vehicle has been incorrectly classified to please contact the company on 1300 381 570 or complete an online form.