NHS England took over responsibility for running the national flu programme in April, but final plans were only issued last week, two months later than in previous years.
GPs face tough new targets and greater scrutiny over how they organise their vaccine clinics, as the government seeks to increase immunisation rates by 50% in one winter.
The RCGP's head of immunisation, Dr George Kassianos, said GPs would need to 'create miracles' to hit the targets because of the late notice.
GPs will have to wait even longer to hear how plans to extend flu vaccination to 650,000 children aged two this year will operate.
Details of the existing programme were set out in a letter from NHS England deputy chief executive Dame Barbara Hakin on 5 June.
Last winter, uptake reached 73% among over 65s, but just 51% in at-risk groups and 40% among pregnant women.
NHS England said this was 'disappointing' and wants the NHS to vaccinate 75% of all eligible patients over the coming flu season, in line with WHO advice. However, only around 100 practices managed to hit these high levels in 2012/13.
Under a raft of new measures to boost uptake:
- GPs have been issued with a 'checklist' and told to review how they organise their flu campaigns.
- NHS England area teams will check whether practices have ordered enough vaccine doses, and monitor performance against the uptake targets.
- Underperforming practices will be singled out and offered support.
Dr Kassianos told GP the 75% target was extremely ambitious, particularly given the late notice.
He questioned how GPs could be expected to order the correct number of vaccine doses when they weren't told in advance which patients would be eligible, nor the targets they should aim for.
'It is not easy suddenly to set the goal so high when we have just received the instructions on the groups at risk and [the] rate to achieve, while we ordered our vaccines last year,' he said. 'The DH is again relying on GPs' ability to create miracles.
GPs need earlier notice
He added: 'We would have liked to have received the influenza programme letter much earlier than beginning of June, as so much has to be planned well in advance.
'We cannot achieve [the target] without early planning. We cannot plan early if we do not have the official letter early.'
He also called for a national flu vaccination awareness campaign to encourage patients to come forward for the vaccine. 'It cannot all be left to GPs,' he said.
The NHS England letter also 'reminds' GPs it is their responsibility to order enough vaccine for eligible patients. It said that 'ordering from more than one supplier is recommended, particularly in the light of last year's experience when disruption in the supply of vaccine from one manufacturer led to localised vaccine shortages'.
GPs received details of the flu campaign on 5 June this year. Previous letters announcing vaccination plans were sent on 28 May 2010, 14 March 2011 and 3 May 2012.
Around 650,000 children aged two will be offered a nasal flu vaccine from this September, in the first step towards rolling out flu vaccination to all children aged two to 16 over the coming years. Further details are due soon.
A spokesman for NHS England said: 'The flu vaccination programme is a widely known routine annual programme. Planning for this year’s programme was already taking place prior to the letter being sent out with practices putting their vaccine orders in some months ago in preparation.
'Previous national flu vaccination awareness campaigns have not resulted in a major change in vaccine uptake. Learning from Northern Ireland however has suggested that communication from practices directly with at risk adults has a greater impact on flu vaccine uptake.'