The company told CW360.com: "There was a problem, [but] it wasn't major. It was identified quickly and no one is out of pocket."
Customers of the bank who tried to use its ATMs on Saturday afternoon reported that the Microsoft NT 4.0 logo was on the screen of the machines.
NatWest has had persistent problems since standardising its systems on NT.
In July 1998, its ATM network failed due to a bug in the NT software, which effectively generated a traffic jam and caused the server to run out of network connections.
The bank has yet to identify the root cause of the latest problem. It told CW360.com that its investigations are continuing.