By Agence France-Presse
The amount of funds involved in the irregular activity totaled "approximately 300 million pesos ($15.3 million)," central bank governor Alejandro Diaz de Leon told reporters.
He said commercial bank customers' accounts were never in danger.
An investigation is under way, the governor said, without indicating if the suspected hackers were domestic or international.
The interbank payments system allows banks to make real-time transfers to each other.
They connect via their own computer systems or an external provider -- the point where the attacks appear to have taken place, Lorenza Martinez, director general of the corporate payments and services system at the central bank, said on Monday.
Martinez revealed that at least five attacks had occurred but, at that time, said the amount taken was still being analyzed.
After the attacks were detected, banks switched to a slower but more secure method.