Responding to the pandemic cost PCTs £340,000 on average, with trusts having to cut services or use contingency funds to meet shortfalls.

Around one in six PCTs (16 per cent) had to cut funding for other services to pay for the response. Others used contingency funds held back from their annual budget, responses from 107 PCTs to a Freedom of Information request show.

The cost of providing equipment, staff and communications varied enormously across PCTs. Four per cent of PCTs spent £50,000 or less, while 9 per cent spent more than £600,000. Overall, costs ranged from £11,100 to £1.7 million.

The true cost to PCTs is likely to be significantly higher than these estimates. PCTs admitted they were not able to account for the costs of staff being redeployed and of staff time spent co-ordinating the response.

• See what your PCT spent on tackling the swine flu pandemic

Deputy GPC chairman Dr Richard Vautrey said that individual PCTs should not have been expected to foot the bill. 'I think a pandemic should be seen as an exceptional circumstance and a PCT should be fully supported by central government,' he said.

'The whole nature of a national health service is that one area should be able to support another, and the unusual financial burden of this episode should be borne centrally.'

Although the DoH provided funding for antivirals and vaccines, PCTs still had to cover the cost of a wide variety of other expenses.

These included support for antiviral collection points, storage and distribution of anti-virals and vaccines and other equipment and consumables.

PCTs also had to pay for communications, advertising and publicity, staff vaccination sessions and additional urgent care support.

Merseyside GP Dr Simon Abrams, medical director at Urgent Health UK, a federation of unscheduled care providers, said that at the height of the pandemic, PCTs had spent money where it was required.

'My impression is that during the spikes, PCTs were much more concerned that care was being delivered than about cost,' he said. 'They were not throwing money around, but they did ensure teams were geared up to address needs.'

David Stout, director of the NHS Confederation's PCT Network, said that PCTs were expected to build up in-year reserves to cover such expenditure. 'PCTs are required to plan for a surplus for exceptional and unexpected events,' he said.

'The costs not covered by the DoH, you would expect contingency funds to deal with.'

PCTs that had not been required to spend these reserves funding swine flu services would be able to fund other patient services, he said.

PCTs in swine flu hotspots would therefore be disproportionately hit.

'Every penny you've spent on this, you won't be able to spend on something else,' he said.

The cost of swine flu

PCTs in England spent £340,000 on average responding to swine flu in 2009/10. But spending varied from £11,100 spent by the lowest-spending PCT to £1.7 million by the biggest spender. PCT funding covered support for antiviral collection points; storage and distribution of antivirals and vaccines; other equipment and consumables; communications, advertising and publicity; staff vaccination sessions; and additional urgent care support. PCTs faced additional costs for redeploying staff and for staff time spent co-ordinating the response.