The National Payments Corporation of India (NPCI) had said over 600 customers had reported losses of at least Rs 1.3 crore due to the breach.
The company, a wholly-owned subsidiary of the Japanese Hitachi, made the acknowledgement following the receipt of final assessment report from payments and information security audit firm SISA Information Security, and said it "regrets" the inconvenience caused.
"We confirm that our security systems had a breach during mid-2016," its Managing Director Loney Anthony said, adding this happened despite following adequate security measures and adopting the standards of internationally- accepted best practices.
The compromise period has been identified between May 21 and July 11. It had come out in public after a slew of banks, including those not serviced by Hitachi, approached customers making either card replacements or ATM PIN changes compulsory.
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Out then, the compromise was suspected to have happened through one of the ATMs of Yes Bank, one of the biggest clients of the company.
"There needs to be a lot more vigilance where there are outsourcing partners to make sure they don't endanger the delivery and system risk, and there's a fair amount of policing as far as outsourcing risks are concerned," he said.
"Hitachi Payment Services regrets the inconvenience caused to banks and its customers due to this lapse in its security infrastructure. We assure you of our highest commitment to building a robust infrastructure in our systems and preventing such cyber frauds in future," Anthony said.
The malware had been able to "work undetected and had concealed its tracks during the compromise period", it added.
The company acknowledged the system-wide trouble, that
was caused due to the lapse at its end, saying banks had to take remedial action like blocking payments at international locations, reduced withdrawal limits, asking for PIN changes and monitoring of unusual patterns.
The company said the actions limited the extent of compromise and claimed that there has not been any "further misuse due to the containment measures deployed by Hitachi Payment Services".