The NHS is setting up a £2bn fund to cover redundancy payments as staff brace themselves for job losses that will to help the service plug a £20bn financial gap.

NHS organisations in England have been told to hold on to 2% of this year's budget, so that the money saved can be spent on one-off projects, such as retraining, setting up new services or making redundancies.

The prospect of reducing staff numbers is looming large, despite all three parties pledging that frontline services will be protected as the NHS's budget is tightened.

Paul Flynn, deputy chairman of the British Medical Association's consultants committee, said: "I would hope redundancy is not the first thing this fund is going to be used for, but it seems job losses will be inevitable. Health is an emotional issue and, during the election, the parties did everything they could to avoid saying anything to indicate they will hit the NHS. But it is naive to think there won't be some effect."

For the first time, this year's national operating framework, in which the Department of Health sets the NHS's priorities, makes clear that England's 152 primary care trusts must retain "at least" 2% of their core funding in 2010-11 – about £2bn in all – to create what NHS officials call "a change fund".

Some hospitals are already trying to reduce their headcount. Cambridge University Hospitals Trust, which includes Addenbrooke's hospital, and the Aldey Hey children's hospital in Liverpool have both told staff there are pay-offs available for those wanting to leave. Southampton Hospitals Trust is losing 400 jobs this year from an 8,000-strong workforce and another 200 next year.

Health secretary Andrew Lansley, who last week suggested that the NHS would have to find "efficiency savings" beyond the £20bn already anticipated, said: "Efficiency savings are being made in order to improve NHS care. I have been clear that money will be reinvested into NHS services."

Health unions immediately warned that patient care would suffer. "Despite promises that the Tories would protect the NHS, just days after the party forms a government, it earmarks a huge pot of money to sack staff," said Dave Prentis, general secretary of Unison.

"Cutting costs and sacking NHS workers will see the quality of patient care fall. Nurses, midwives and healthcare assistants work as part of a team. They depend on other staff for support so they can do their jobs. So-called back office work is crucial to the smooth running of the NHS. What would you prefer nurses to be doing? Caring for patients, or typing up medical notes?" said Prentis.

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