The extension to the federal government's "no jab, no play" policy has been welcomed by the ACT chief health officer but condemned as draconian by parents who have reported negative reactions to vaccines.

The changes mean those with a conscientious, including religious, objection to having their children vaccinated will no longer be eligible for the child care benefit, child care rebate or the Family Tax Benefit Part A supplement.

The benefits are worth an estimated $7000 per family on average each year for those with young children.

A medical exemption would continue to apply but its criteria has been tightened.

The latest figures showed 393 children were recorded with a conscientious objection to vaccination as of September.

The figure equates to 1 per cent of all ACT children aged six and younger, the lowest rate since March 2012 and the second lowest in the country behind the Northern Territory. But the ACT trend has been reflected nationally, with 8000 fewer children registered for conscientious objection than a year before, a rate drop from 1.79 per cent to 1.43. Rates were falling even before the Coalition's April announcement.

As the new changes apply to all those aged 19 and younger, the number of affected Canberra children and youth would easily exceed 400.

Australian Vaccination-Skeptics Network president Tasha David said the changes would particularly hurt low-income families who were breaking no law by choosing not to vaccinate their children.

"We're not saying everyone shouldn't vaccinate, we're saying we have healthy children without reliance on pharmaceutical products," she said.

Ms David, who has eight children, said they would be unable to qualify for the medical exemption despite her doctor saying they had a genetic susceptibility to adverse reactions to vaccines.

Shayla Plosko from Kaleen, a former senior auditor with the public service, had her elder son, aged three, registered for conscientious objection but decided there was no point doing so for her now 10 month old son after the federal government's new plans were announced. The family will lose about $750 per child per year for several years, she said.

Ms Plosko said she and her partner were fully vaccinated but had, after research, decided not to vaccinate their children. About two years ago she and her partner each had a serious and extended reaction to vaccines and contracted whooping cough, which she said they passed on to their unvaccinated elder son, then five months old.

Her son recovered in three days, she said. "Both of us had the [whooping cough] vaccine, and we got it."

"The financial impact is not what bothers me or most people that do not vaccinate, it's the blanket approach to vaccinating everyone with the same vaccines without taking into consideration any other conditions or health issues," she said.

The federal health department said severe complications from whooping cough, including pneumonia and brain damage, occur almost exclusively in unvaccinated people.

ACT chief health officer Dr Paul Kelly said any initiative, such as "No Jab, No Pay", which aimed to increase immunisation rates should be applauded.

There was an epidemic of whooping cough (pertussis) in Australia between 2008 and 2012, and 2015 was also a bad year, with the notification rate at higher levels than in any year between 1991 and 2008, according to the National Notifiable Diseases Surveillance System.

A federal health department spokeswoman said whooping cough would continue to circulate despite high immunisation coverage rates, but vaccine remained the best defence against the disease.

"The vaccine is not always completely effective and the protection provided by [it] also wanes over time, leading to a build-up of susceptible people," she said.

"The whooping cough immunisation programme is effective in preventing severe morbidity and mortality among infants."

There have also been 78 cases of measles notified nationally in 2015. Of the 42 cases where vaccination status was known, 38 involved people either not vaccinated or only partially vaccinated.

Families have until March 3 to have their children up to date on their immunisations or on a recognised catch-up schedule to retain the benefits.

Canberra has the highest immunisation rates in the nation, with 93.3 per cent of children aged 12 to 15 months fully immunised, and 90.8 per cent for those aged 24 to 27 months.