A whooping cough epidemic sweeping the country has claimed the life of a 6-week-old Christchurch baby.

Canterbury District Health Board medical officer of health Ramon Pink yesterday confirmed the baby died of the disease in Christchurch Hospital last month.

The baby, who was born prematurely, had been scheduled to go to Auckland's Starship children's hospital but had been too sick to travel.

"It was a very difficult experience for [the family]," Pink said.

One other pertussis death has been reported this year. It involved a 3-year-old unimmunised child with underlying health conditions from another part of the country.

"It's a tragic reminder, I think, of the seriousness of whooping cough. It's a significant issue and showing no signs of abating. It is a national epidemic," Pink said.

About 5389 cases of whooping cough, also known as pertussis, have been reported throughout the country this year, including 1150 in Canterbury and 52 involving children under 1.

Yesterday, Minister of Health Tony Ryall said a vaccine would be available nationwide from January 1 to help pregnant women protect their babies.

Free vaccinations had been available to Canterbury women since April after the disease began spreading through the country in May last year. About 1500 women had taken up the offer.

Ryall said international research showed that vaccinating mothers during pregnancy was the most effective way of protecting babies before they were immunised.

About 70 per cent of babies who contracted the disease during their first few weeks of life caught it from their parents or other close family members.

He encouraged parents to have their children vaccinated at 6 weeks, 3 months and 5 months.

The free vaccine would be available to women between 28 and 38 weeks of pregnancy from their GP until the pertussis outbreak ended.