Family doctors are calling on Scotland's chief medical and nursing officers to step into a row about administering the injection and oblige NHS nurses and midwives to help vaccinate expectant mothers.
The Royal College of Midwives Scotland (RCM) says GPs are funded to perform vaccinations along with other public health duties and administering them can make antenatal appointments much longer.
But GPs are worried that some women will not show up after being sent by their midwife to attend a separate medical appointment for their vaccination.
It means the opportunity to prevent their babies catching the potentially fatal illness could be missed at a time when the numbers contracting the illness are at their highest level for at least 20 years.
Gillian Smith, director of the RCM in Scotland, said: "Until recently whooping cough was something that had never been discussed for midwives to do.
"All midwives understand the importance of it, but what do they drop off in order to do it? If you just had a redistribution of the finances and some team working it could all work out quite fine. But do midwives short-change women who are pregnant and need their support so they can give the whooping cough vaccine when the finances are being given to the general practice?"
A whooping cough outbreak hit the UK last year leaving infants at risk due to the small size of their lungs. In England and Wales more than 10 babies have died.
Experts advised both the Scottish and Westminster governments to offer pregnant women the vaccine last autumn in order to give newborn infants some protection against the germ until they are old enough to be immunised.
Dr Dean Marshall, a Lothian GP and member of the British Medical Association Council in Scotland, said reluctance among midwives to give the vaccine was widespread. He added: "This problem first surfaced when there was pandemic flu. That was potentially a major public health issue and midwives were refusing to vaccinate pregnant women [against swine flu] despite all the advice from medical experts. That has carried on with the whooping cough vaccine."
He said midwives would discuss the vaccine with their patients and book appointments for them, but refused to administer the injection. "I assume some of them have their own personal views about vaccinating pregnant women but at the end of the day they work for the NHS and the NHS is carrying out a public health policy," Dr Marshall said.
Ms Smith said midwives were not concerned about the safety of the vaccine, but the problem was the extra workload. She said administering the flu vaccine added 10 minutes to a consultation, a problem in busy clinics.
She said the money for delivering such public health measures was provided to GPs in their contract. She added if it was transferred to community midwifery services, or GP practice staff were loaned out to antenatal clinics, then midwives could make the most of the opportunity and offer patients the vaccine at antenatal appointments.
Dr Marshall said giving the vaccine added to the workload of surgeries and meant patients having an extra appointment which they might not attend.
The issue will be discussed at a major British Medical Association (BMA) conference in Glasgow next Friday.
A motion being put to GPs calls on Scotland's chief nursing officer and chief medical officer to jointly instruct health boards to ensure all relevant health board employed staff are obliged to administer influenza and whooping cough immunisations in pregnancy. If the motion is passed, the BMA's Scottish General Practitioners' Committee will take forward the concern.