In a statement, RBS says: "We are currently experiencing technical issues which mean that a number of customer account balances have not yet been updated and some of our online services are temporarily unavailable."
A similar message appears on the NatWest Web site, with the bank adding: "We are working hard to fix this issue as soon as possible and will keep you updated on progress. We are experiencing very high call volumes as a result."
In a later update, RBS has revealed that the issue "was caused by a failure of our systems to properly update customers' balances overnight. The main problem customers are having is that where people have had money go into their accounts overnight, there may be a delay in it showing up on their balance."
The problems have been ongoing for several hours, with NatWest first acknowledging the issue on its Twitter feed at 08.43, eliciting responses from customers complaining that payments have not been processed and wages not paid.
By 13.32 there appeared to be no fix in sight, with RBS stating on Twitter it hoped to have resolved the issue "within the next few hours".
The ongoing crisis has forced the bank to take drastic measures, promising to keep over 1000 branches open until 19:00BST on Thursday to assist short-changed customers.
Daoud Fakhri, a senior analyst at Datamonitor says the episode is emblematic of wider problems facing the banking sector as a whole.
"Many providers, being early adopters of IT systems when the technology was still in its infancy, have been left saddled with inflexible core systems that are often several decades old, and that are increasingly unable to cope with the demands being placed on them," he says. "The growing expectations of consumers around online and mobile banking means that the tensions between the provision of ever more sophisticated services and the capability of core systems to satisfy these demands are close to breaking point, and this increases the likelihood of episodes such as the NatWest mishap happening again.
Separately, the Web site of Norwegian bourse Oslo Børs has been knocked off line, apparently by a DDoS attack. Spokesman Per Eikrem told local outlet NTB that the hit is only affecting the exchange's site and not its trading, messaging or monitoring systems.