Up to 10,000 Sydney motorists may have been wrongly billed after Melbourne's CityLink toll road stopped differentiating between NSW and Victorian number plates.

The error, which occurred when CityLink upgraded its electronic tolling system before Christmas, was picked up only late last week.

It was discovered that motorists in NSW who have the same number plates as Victorian motorists were charged when their counterpart across the state line travelled through CityLink.

The maximum charge for any trip on CityLink, 22 kilometres of toll road, is $7.20.

Transurban - which owns CityLink, as well as Sydney's M2, the Lane Cove Tunnel and shares in the Eastern Distributor, M7 and M5 - has already started refunding some customers.

In a statement this afternoon, CityLink's group general manager, Elizabeth Mildwater, said: "The issue relates to licence plate numbers that exist in both New South Wales and Victoria.

"We don't require motorists in NSW to contact their toll provider if they think they have been incorrectly charged, because CityLink has implemented a manual review process to reverse charges," she said.

"CityLink has found some instances where the automated system has charged the New South Wales vehicle instead of the Victorian one.

"They have already identified how this occurred and have stopped it from happening any more.

"CityLink apologises for the inconvenience caused and would like to assure affected customers that they will not be out of pocket."