Dr Peter Holden, the GPC's lead negotiator on pandemic flu, said the cost per dose had not even been discussed with the DoH.
Media reports suggested that the BMA has requested £7 per dose, which for England's entire 50 million population to receive twice, as recommended, would add up to £700 million.
But a BMA spokesperson said that this figure was 'rather inaccurate' and that negotiations were ongoing.
'The seasonal flu jab costs £7.51, but because the swine flu vaccination programme will be on a much larger scale there are also other issues to consider, not least the workload.
'We want to ensure GPs are still able to provide a good service to patients ill with conditions other than swine flu and that's why we are continuing to negotiate with the government on this issue,' they added.
Ian Dalton, England's director for flu resilience, told GP: 'In terms of the income issues, we don't want GPs to lose out financially from flu.
'We don't know how flu will develop, because that's the nature of the flu virus.
'We have some possibilities of surges later in the year and we need to prepare for those. But, equally, nobody can tell us with any certainty what will happen with any exactitude.'
Earlier this month BMA Northern Ireland requested £55 million to tackle the pandemic among its 1.75 million population, but the assembly government refused.
Extrapolating BMA Northern Ireland's estimated cost to cover England's population, at £31.40 per person, the figure spirals to £1.57 billion.