Train passengers have been warned they could be mistakenly overcharged for their journeys until late June.
The issue has been affecting people using contactless payments on some c2c services between Essex and London.
Automatic refunds were being arranged for those who had been charged an additional £3 per trip, the train operator said.
It expected the situation to be resolved by 29 June.
Only journeys to or from stations outside Zone 6 – and that started at either Fenchurch Street or Liverpool Street in London – have been affected.
'Extremely sorry'
Transport for London (TfL) has been working with c2c to resolve the issue, which was first reported on Wednesday.
The first round of refund payments would be made over the weekend, c2c added.
Commercial director Eleni Jordan said a "technical issue" was causing the overpayments.
"We are extremely sorry for any inconvenience caused and appreciate our customers' understanding and patience," she said.
