Around 600,000 RBS transfers were affected by a technical glitch on 17 June, which caused payments to be delayed for days, a spokesman has said.
The company responded to hundreds of complaints on Twitter when it found out about issues with overnight transfers including benefits and tax payments for RBS, NatWest, Ulster Bank and Coutts customers.
A spokesman for the state-owned bank said: "We are working flat out to get these payments updated for our customers no later than Saturday [20 June]."
He added that RBS had fixed the problem and apologised to its customers for the inconvenience. The bank stated it was aware of the effect the glitch had on debit or credit applications to customer accounts.
"To any customers concerned about the implications of this issue, we advise them to get in touch with our call centres or come into a branch where our staff will be ready to help," the spokesman said.
RBS added it was working to resolve the issue as quickly as possible. The bank is currently providing temporary credit to customers as a solution. "We will ensure no customers are left out of pocket as a result of this issue," it stated.
Although a relatively small number of transfers were affected considering the size of RBS, the patience of customers was tested because the bank has experienced many issues with transactions over the past few years.
In November 2014, RBS was fined a total of £56m (€78.2m, $88.1m) by the Financial Conduct Authority and the Prudential Regulation Authority after being hit by a cyberattack in 2013 and many other online issues that affected its customers.
Angry customers on Twitter have said they would switch banks and expressed desperation and concerns over delayed payments. Customers also queried RBS and NatWest how the bank was going to deal with charges imposed by third parties after people missed transfers because of the issue.