A 'deep-rooted resistance' to vaccination during pregnancy means many women will be left unprotected this winter, according to RCGP health protection lead Dr Maureen Baker.
She called on GPs and midwives to encourage pregnant women to be vaccinated. Last winter, just 25.5% of pregnant women accepted the flu vaccine.
The warning follows the DH's decision not to advertise the flu vaccine nationally to the public this season.
Dr Baker said: 'We continue to worry about vaccination rates in pregnant women. Again, obstacles to vaccination are incompletely understood, but I feel there are a number of factors.
'Firstly, women may not be pregnant at the time of the vaccination campaign and, even if they are, they are often not individuals who regularly receive the vaccination.'
However, the causes of poor uptake extend beyond the lack of awareness, said Dr Baker. 'I believe there is also deep rooted resistance to vaccinations in pregnancy - this is a view also held by some health professionals.'
The RCGP will be issuing a bulletin next week to alert members to the risks of flu to pregnant women. It will summarise the latest scientific evidence for the vaccine's safety and effectiveness when used during pregnancy.
Dr Baker also warned there may be complacency among the general public following a mild winter in 2011/12 and low flu activity.
Meanwhile, the college's immunisation lead Dr George Kassianos said it was 'regrettable' the DH will not run a flu awareness campaign in England this winter. But he said the DH target to vaccinate 75% of at-risk people by 2013/14 was still achievable.
He said: 'A national public advertisement campaign could have helped us enormously but the lack of it will not deter general practice from achieving the target. No other country in the world can deliver vaccinations so fast and so efficiently as UK general practice. I am very optimistic.'