The London congestion charge system went down yesterday after IBM took over the contract from Capita.
Customers that registered online to pay congestion charges could not access the system because of a "technical glitch" on Monday 2 November.
Transport for London (TfL) transferred data on the system from Capita systems to IBM over the weekend. The transfer went well but left registered users unable to pay the charge.
A TfL spokeswoman said the problem was sorted out by the afternoon. "Nobody [in the group affected] will be penalised. Another reason it is not a big issue is that charges can be paid the day after.
"We apologise for the problems that some customers may have experienced in accessing the Congestion Charge online payment accounts. These were resolved and all of the new IBM systems are up and running as they should be.
"During the glitch, customers were still able to pay their charge via the other payment channels available, for example, through the call centre, via SMS and at their local shops," she said.
IBM's takeover of the operation of the congestion charging scheme includes an upgrade of the computer systems, which will save TfL £200m over the life of the current business plan.