The taxpayer-backed lender was among eight global banking giants, including Barclays and Deutsche Bank, fined a record €1.7 billion (£1.4bn) after a European Commission investigation into Libor-rigging.
RBS, which is 81% owned by the Government, is estimated to have avoided more than €160m (£130m) in fines from the EC because of its co-operation with the investigation.
It was one of the banks that agreed penalties with the EC for its role in the attempted rigging of the Yen Libor and Euribor - the Tokyo and euro area equivalents of the London interbank offered rate (Libor). The rates are used to set the price of trillions of dollars of products, including mortgages.
The development came after RBS's embarrassing IT systems failure which resulted in millions of customers being locked out of their accounts.
RBS said the fines were "covered by provisions already made" and management had strengthened oversight of how the bank submits information to Libor and other trading rates.
Barclays and UBS were found to have attempted to rig European rates, but avoided a fine after blowing the whistle on the Euribor.
The sanctions - the first from the EC on rate manipulation - are the highest yet for European antitrust enforcement.
And Joaquin Almunia, the commission's vice-president in charge of competition policy, warned that further fines were on the cards as three banks and one broker had refused to settle on other claims being investigated by Brussels.
"This will not be the end of the story," said Mr Almunia, who added that foreign exchange markets were also facing an investigation for potential manipulation.
"What is shocking about the scandals is not only the manipulation of benchmarks, which is being tackled by financial regulators worldwide, but also the collusion between banks who are supposed to be competing with each other," he said.
"Healthy competition and transparency are crucial for financial markets to work properly, at the service of the real economy rather than the interests of a few."
UBS avoided a massive €2.5bn (£2.1 bn) fine after flagging up the Yen Libor cartel with the EC.
RBS chairman Philip Hampton said: "We acknowledged back in February that there were serious shortcomings in our systems and controls on this issue, but also in the integrity of a very small number of our employees.
"Today is another sobering reminder of those past failings and nobody should be in any doubt about how seriously we have taken this issue."
Deutsche Bank received the biggest fine of €725.36m. The other financial institutions involved were Societe Generale, JP Morgan, Citigroup and the UK-based brokers RP Martin.
The EC fines brings the total penalty tally for banks' benchmark manipulation to $5.8bn, a sum that is expected to continue to rise as regulators conclude probes and private court cases stack up.
Barclays and RBS have already been fined for rigging the price of interest rate products based on the London interest rate market, Libor.
Barclays paid £290m and RBS £391m for their involvement.
That was followed by the departures of its chief executive, Bob Diamond, and its chairman, Marcus Agius.
Barclays said it "voluntarily" reported the latest wrongdoing to the Commission and "co-operated fully" with the investigation.