Pharmac is extending funding for whooping cough antibiotic azithromycin to help combat New Zealand's latest epidemic.

More than 1700 confirmed, probable and suspected cases of the potentially fatal bacterial disease have been notified to health authorities this year, compared with 241 in the same period last year.

"The current treatment, erythromycin, had troublesome side effects in young babies - the very group of children most at risk from whooping cough," said Dr Emma Best, a paediatrician at Starship children's hospital in Auckland.

"Azithromycin is as effective and is able to be given once a day, as well as in a shorter course for both treatment and prevention if a little baby is exposed to whooping cough," she said.

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Pharmac medical director Dr Peter Moodie said: "Our funding decision means that children under one year will be able to be treated with azithromycin if they have whooping cough, or if they come into contact with someone with whooping cough. This will help give them additional protection from infection."

Vaccination injections are recommended at six weeks, three months, five months, four years and 11 years.

"Until babies are fully immunised, adults pose the most risk to them. About 70 per cent of babies with whooping cough catch this infection from parents or other close family members," said paediatrician Dr Cameron Grant.

"Of the infants admitted to Starship [children's hospital in Auckland] with whooping cough, one in 10 will end up in intensive care and, of these, one in six will die or be left with brain or lung damage."

The last whooping cough epidemic of similar scale was in 2004/05, although there was a smaller one in 2009. They typically occur every four or five years.

Pharmac will begin funding azithromycin for whooping cough from June 1.