The announcement was made ahead of the Bank of England’s next decision on the interest rate, with some predictions suggesting this could drop below zero.

RBS owns NatWest and the state-backed bank has written to 1.3m business clients to say ‘global interest rates remain at very low levels’, and to advise account holders that this ‘could result in us charging interest on credit balances.’

Personal customers are not affected, but charities and community groups are counted as business clients and so would potentially face the charges, the banks said.

Mike Cherry, national chairman at the Federation of Small Businesses (FSB), said the warning from Natwest and RBS will be deeply concerning to small firms, particularly as the federation’s latest research shows small business confidence is already at a four year low.

‘When the Monetary Policy Committee meets next week to decide on interest rates, we would call on them to do everything possible to consider the implications of changing interest rates for smaller firms and the self-employed looking to maintain or grow their business,’ Cherry said.

The FSB is also calling on all finance providers holding deposits from small businesses do everything they can to update customers concerned about any changes to their Business Current Account (BCA).

Cherry said: ‘We would also encourage small firms themselves to take action and consider whether it’s worth switching to a more competitive BCA. One resource to consider is the Business Banking Insight website, which compares BCAs offered on behalf of every bank operating in the UK, to see whether there’s a better deal for your business.’

UK interest rates have been fixed at a record low of 0.5% since March 2009. Economists are forecasting that the Bank of England could reduce rates to 0.25% or even lower when it meets next week.