DOCTORS have warned parents to keep newborn babies at home to protect them from a whooping cough epidemic triggered by the "chardonnay set and alternatives".

There have been 4580 cases of whooping cough so far this year, new data from NSW Health reveals.

Northern Sydney and South Eastern Sydney have led the way in this year's resurgent epidemic, recording the highest incidence of whooping cough, with 669 and 522 cases respectively. The Illawarra region was next highest followed by Western Sydney and Southern Sydney.

National Centre for Immunisation Research and Surveillance deputy director Dr Rob Menzies said it was unsurprising which suburbs had the highest rates of infection.

"It's a phenomenon where highly educated people feel they need to do their own research on what is best for their child and there is scepticism of official government policy," he said.

"But a lot of people are likely to find wacky anti-vaccination sites where a lot of the information is distorted. It is not helping that people opt out of vaccination.

"It puts their children at risk and it puts other people's children at risk."

The epidemic has infected one in five children at a school near Lismore, prompting doctors to warn parents to cocoon newborns to minimise the risk.

"With vaccination rates so low in this area we say to the mothers of newborns, do not take them out in the community," local paediatrician Dr Chris Ingall said.

"We're appalled at how many kids are getting whooping cough because the chardonnay set and the alternatives don't vaccinate their children."

Areas with low vaccination rates had 300 per cent more cases of whooping cough between 2008 and 2010, according to figures from NSW Health.

The national average of conscientious objectors to vaccinations is 1.1 per cent but, in Mullumbimby, 21 per cent are conscientious objectors, as are 16 per cent in Byron Bay, meaning that as many as one in five families have children who are unvaccinated.

The epidemic of 2008-09, which affected 12,000 people and claimed the life of four-week-old Dana McCaffery from Tweed Shire, began on the north coast and spread to affluent Sydney suburbs such as Bondi, Vaucluse, Coogee and Manly, where up to 8 per cent of children are not vaccinated.

Dana McCaffery's parents Toni and David now have baby Sarah, 14 weeks, who they are cocooning, until she has all three shots to cover her against the epidemic.

"We know it is out there and rather than it be a silent predator, we are not going out and not working," Mrs McCaffery said.

Her husband is a schoolteacher at St Joseph's Primary School in Alstonville which is in the grip of a whooping cough epidemic.

Doctors say adults, whose shots have worn off, can pass on the disease to infants.

"We have tried to make some sort of difference ourselves, when we were standing over our daughter's grave and thought people need to know about this, but still only 18 per cent of adults are vaccinated," Mr McCaffery said.