Ian Dalton, DoH national director for flu resilience, was asked by the GPC to ensure a consistent message reached all parts of the NHS.
GPC chairman Dr Laurence Buckman said there was no evidence pregnant women should not have the jab, but that NHS staff were giving out mixed messages.
'There is evidence that pregnant women can, if they contract flu badly, end up on a ventilator,' he said.
'It is the responsibility of the NHS to make sure it puts out a consistent message.
'We have spoken to flu czar Ian Dalton about issues where midwives and occupational health services are reluctant to vaccinate pregnant staff.'
GPC Scotland chairman Dr Dean Marshall said that BBC polls roughly reflected anecdotal evidence that uptake of the vaccine in priority groups was approximately 50 per cent across the UK.
He added that there was a 'mixed picture' with no evid-ence of different uptake in affluent or deprived wards.