Transurban is making millions of dollars each year charging motorists fees that are only meant to cover the toll road operator’s costs, leaked documents from the company show.

Under its contract with state governments, Transurban is only meant to charge fees reflecting the costs it incurs.

But nationally in 2016 it charged its customers fees totalling $147 million - about 7.5 per cent of its revenue.

The company denies making a profit from customer fees but, questioned on Monday over its charges, said it would next week announce the removal of a number of them.

As well as tolls for using CityLink, Transurban charges its Victorian customers fees for a range of services including pursuing unpaid tolls, matching images of cars without a valid tolling device, and replacing eTags.