Despite the losses, the bank is set to announce it will pay bonuses of £1.3bn to its staff.
The bank’s chief executive, Stephen Hester, however, has said he will not take his own bonus.
The UK taxpayer owns 84% of RBS after the government bailed out the bank at the end of 2008.
Mr Hester told BBC Radio 4’s Today programme RBS had lost out by not paying bigger bonuses.
“We’ve had a small experiment in this respect… some of our best-performing people have been leaving in their thousands,” he said.
“The people who left us last year, I believe, would have increased our profits by up to a billion pounds beyond the ones that we’ve got.”
One other controversial topic for the banks has been its role in lending to business and home buyers.
Mr Hester again defended the bank’s approach. He said he was satisfied that RBS was fulfilling both the letter and the spirit of its lending commitments, saying it had beaten its target for mortgage lending.
He said the bank had not, however, reached its target for small business lending, partly because businesses, he said, were focused on paying off debt.
Bad debts rise
The loss figure is lower than the £5bn many experts were expecting and is well below the £24bn it lost in 2008.
Bad debts rose sharply to just short of £13.9bn from £7.4bn in 2008, but the bank says it thinks these have now peaked.
Mr Hester said he expected the bank to return to profit next year.
RBS is the second major UK bank to report 2009 results, after Barclays announced record profits of £11.6bn.
Lloyds Bank will report its results this Friday.