Shares in the 80%-taxpayer-owned bank dropped 3% on the news.
RBS boss Ross McEwan said: "The scale of the bad decisions during that period [the financial crisis] means that some problems are still just emerging."
RBS said its executive committee would not receive a bonus for 2013, Mr McEwan has waived his bonus for 2013-14.
RBS said on Monday the £3.1bn it planned to set aside would be used to settle claims relating to mortgage products, PPI claims and interest rate hedging.
It would allocate:
RBS chairman Philip Hampton said: "RBS did suffer more than most banks in the crisis and these charges today represent an extra clearing-up of the mess that was created in the bank in the run-up to the financial crisis of 2008."
By Robert PestonBusiness editor
The announcement of the new provisions came near the end of share dealing in London.
Business Secretary Vince Cable said: "It's an absolutely shocking story that the British taxpayers are still paying for the excesses of this bank in the boom period before it collapsed."
Ian Gordon, from Investec Securities, said the news was not entirely unexpected, but the amounts involved were.
"Some of this is a pull forward of future bad news and some of this is additional," Mr Gordon said.
"Most of the items aren't surprising, but the amounts are at or above the top end of expectations."
The cumulative amount set aside to cover the mis-selling of PPI, payment protection insurance, alone, is now £3.1bn, said RBS.
RBS, has also, in common with most of its rivals, been fined for fixing the key Libor interest rate and has suspended traders amid an investigation into alleged rigging of the foreign exchange markets.
The BBC learned earlier this month that general discussions about bonuses had taken place with shareholders, including UK Financial Investments, the body that manages the government's shareholding in the bank.
But, in an interview with the BBC on Monday, RBS chief executive Ross McEwan explained why the most senior executives would not be receiving bonuses this year.
"This is about leadership," he said. "When you look at what we're having to put aside for past activity regarding litigation and conduct, I said to the team, 'I am sorry, I just cannot justify the payment of a bonus.'"
He added most of the current leadership had nothing to do with past wrongdoing, but said they needed to "set the standards".
But Mr McEwan said that when it came to paying 200% bonuses to attract and keep talented staff, "We need to make sure that, whatever the market does, we are in a position to follow it.
"We are not the leaders on pay, we just need to stay within touching distance of those we have to compete with to get the talent."
The controversy over bank bonuses flared up in Parliament earlier this month, with Labour demanding Chancellor George Osborne block any attempt by RBS to pay bonuses of up to double its bankers' annual salary.
In 2008, the government bailed out RBS with £46bn of public funds, and now owns just over 80% of the giant bank.
Since then, the bank's share price has tumbled to less than one-third the price the government paid for it.
There are questions over whether the government will be able to recoup that money.
BBC business editor Robert Peston said that investors and politicians had told him they think it is unlikely taxpayers will get all their money back.
RBS may face full-year losses of up to £8bn, after the bank said it needed another £3.1bn for claims relating to the financial crisis.