The DoH said GPs only need to obtain consent for the vaccine itself and do not need explicit consent for the swine flu component. But the GMC and the Medical Defence Union (MDU) advised GPs to explain this to patients who had previously refused the vaccine.
One GP leader warned there was a risk seasonal flu vaccine uptake could be hit.
This year's trivalent seasonal flu jab contains swine flu antigens because experts believe swine flu will circulate this winter.
GMC assistant director of standards Jane O'Brien said it would be wise to explain this to patients who previously rejected the vaccine. She said: 'If you know a patient has previously refused the single swine flu vaccine, it's likely they would want to know this year's seasonal vaccine includes the swine flu strain.'
However, GPs must be careful not to put pressure on patients to accept advice. An information leaflet has been produced to explain the contents of the vaccine.
A DoH spokesman said: 'Like previous years, this year's seasonal flu vaccine contains protection against three strains of influenza in a single dose.
Because it is a single vaccine, only one consent is needed from patients.'
But Suffolk GP Dr Fergal O'Driscoll said: 'Lots of patients refused that specific component last year when offered it. I'd be anxious about including this without specific consent.'
Dr O'Driscoll said it would be a 'dangerous precedent' for the profession not to check these patients knew the vaccine contained swine flu antigens.
GPC negotiator Dr Peter Holden said 'there is always the possibility' vaccine uptake could be hit, although any fears over the vaccine were unfounded.
Dr Udvitha Nandasoma, a MDU medico-legal adviser, said GPs 'may wish to check patients' understanding of the vaccine before they administer it'.
RCGP immunisation lead Dr George Kassianos said: 'We should not lose any opportunity to discuss the contents of this year's influenza vaccine.'