Bosses say the operator’s parent company, Trenitalia, was targeted in the attack and this has since caused issues with c2c systems.
Customers have this week experienced problems buying tickets from offices at statiosn across south Essex as a result of the attack.
Passengers are urged to book train tickets in advance until the issue is resolved.
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A spoeksman said: “Trenitalia c2c is working with our suppliers to resolve the technical issues, which will allow tickets to be sold at c2c ticket offices.
“We apologise to any c2c customers that have experienced issues buying tickets over the last few days.
“In the meantime, we would like to reassure customers that tickets can be purchased at our ticket machines or alternatively bought in advance using the c2c App and free Smartcard.
“Staff at our stations will also be available for any queries or technical support.”
Stations affected by the issue include Chalkwell and Leigh, with Southend West MP Anna Firth saying earlier this week she was aware of the problem.