Data released last week show how the DoH made a loss of £128 million on surplus swine flu vaccine purchased last year.
Of this, the DoH spent £30 million on vaccine due to be delivered in 2010/11 when the pandemic was largely over.
The department has also written off antivirals worth £72.9 million, after admitting it has no evidence that these drugs were stored correctly by the NHS.
These drugs have been retained for potential future use, but may have to be destroyed as it is unclear whether the NHS will be able to use them without documentary evidence.
Figures in DoH resource accounts for 2009/10 show £470 million was spent on antiviral drugs last year in total.
In addition to the £200 million loss from swine flu, a further £23.5 million was lost on date-expired vaccine doses including those for avian flu purchased in previous years.
GPC negotiator Dr Peter Holden said the figures were 'peanuts' in comparison to the cost of a severe pandemic.
'It's not just about keeping the nation at work, but keeping society running,' he said. 'If you want 100 per cent supply guarantee, it comes at a price.'
A DoH spokeswoman said: 'At the start of the outbreak, there was no way of knowing how virulent swine flu would be. The department took the necessary steps to deal with a worst-case scenario in which it would have been necessary to vaccinate every member of the population twice. However, as the spread and virulence of the outbreak was less severe than first anticipated, less vaccine was needed.'
A global surplus of swine flu vaccine meant the DoH could not sell-on the excess stock. It plans to retain the surplus, which is still clinically effective, as a 'strategic reserve'.
The DoH ordered 120 million doses of swine flu vaccine, but was left with more than 30 million excess doses because there was no break clause in its contract with manufacturer GSK.
It agreed to purchase H5N1 avian flu vaccine from GSK as part of the deal to end the contract. At the time, then health secretary Andy Burnham described the deal as 'good value for the taxpayer'.