The Central Bank of Mexico has not provided the names of all the institutions affected nor the exact amount of money that was stolen, but some local media report at least $300 million Mexican pesos (about $15 million U.S.).
In the most famous SWIFT hack, thieves made off with more than $100m (£73m) from the Bank of Bangladesh using falsified transfers that were sent by hacking the bank's internal systems.
He said the amount not accounted for may be between 350 million pesos and 400 million pesos. "Some of the transfers were stopped, and the funds are now being returned", she said.
"Probably the largest ever", Gricha Raether said, a financial technology expert managing a US -based fintech company in Mexico City. "We're taking corrective and mitigating action".
Mexico's central bank and regulatory agencies said they are not sure whether the problem with settlement transactions among banks was the work of outside hackers, an inside scam or errors.
He later said in a radio interview that all the evidence, which is so far only partial, pointed to a cyberattack.
Like the SWIFT attacks, those using Mexico's SPEI interbank transfer system did not compromise the core network itself, instead manipulating the systems banks use to interact with it.
Hackers may have had help inside bank branches, since such big cash withdrawals are uncommon, one source said.
"In terms of the security of the bank's offices, I think that is part of the analysis that each bank is doing", Martinez told Reuters.
Lorenza Martinez, head of Banxico's payment system, told Reuters that five lenders had seen unauthorized transfers and that they are now running analysis to see if malicious insiders were involved.
The central bank then required all banks to take additional security measures, slowing some time-sensitive transactions like debit card purchase approvals and e-payments to a crawl.
Depositors won't be affected, but the banks themselves could take a hit on the missing money.
Mexico's SPEI system is a domestic network similar to the SWIFT global messaging system that moves trillions of dollars each day.
After the vulnerability was detected, the three banks abandoned the outside contractor that supplied the defective software and changed over to the central bank's own settlement system.
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