The attempted multi-million pound theft at Santander involved fitting a keyboard video mouse (KVM) device to a computer within the bank's Surrey Quays branch, the Metropolitan Police has said.
This would allow the suspects to view the desktop contents of the bank computer and take control of it from a remote location.
The Met said: "Yesterday's time-critical, dynamic response was achieved by working in partnership with the banking sector, thwarting a very significant and audacious cyber-enabled offence."
The 12 men arrested are being held at a London police station following searches at a number of addresses across the capital.
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