"[They] directly accessed a computer system, namely the computer systems of Flight Centre and Mastercard Cash Passports ... and dishonestly and without claim of right caused loss to Flight Centre," the charging documents read.
Flight Centre has chosen not to discuss the breach of its computer system, saying only: "As the case is currently before the courts we cannot comment."
It would not clarify whether the two accused were Flight Centre employees, whether customers' details are safe, or if its computer systems have been made more secure since the breach.
A spokeswoman for MasterCard said: "If MasterCard cardholders have questions about their accounts or suspect they have been a victim of a fraudulent activity, they should immediately contact the financial institutions that issued their cards."
An earlier version of this story was illustrated with a file photo. The people pictured had nothing to do with this alleged crime.