His comments come after Australia announced a new policy to be introduced next year that would cut a number of child and family benefits from parents who refuse to vaccinate their children. The legislation - dubbed 'no jab, no pay' - has been met with a mixed response.
Prime Minister John Key has already ruled out following in his Australian counterpart Tony Abbott's footsteps, saying he didn't want to remove the element of personal choice from parents.
But Dr O'Sullivan said he would not be deterred by the naysayers.
"I don't know how many deprived children I've dealt with who've been incredibly sick recently," he said.
"I believe a person who's working at the coal-face of the impacts of diseases that are preventable by vaccination on a weekly, if not daily basis, I believe this is a positive step.
"It doesn't address some of the deeper issues, which are children living in poverty, but we do have to look at, until we fulfil that goal, which I think should still remain the goal of every New Zealand citizen, we should be looking at ways to mitigate the current situation that these children are living in."
Children living in cold, damp homes, who were not vaccinated were at a high risk of contracting diseases such as pneumonia, he said.
"I guess people might say that this could contribute to further poverty among children, [but] I don't necessarily believe it would," Dr O'Sullivan said.
"Just as we have an initiative to ensure that benefits are spent in the right place, ie rent, food, power, water, I don't think that should be used as a scare tactic to say we shouldn't be bold and we shouldn't do things that target resources to the needs of the most vulnerable."
He suggested a system where a family benefit would have a monetary base-amount, and parents would receive incentives if they met certain conditions, such as vaccinating their children and enrolling them to early childhood centres.
However, it shouldn't just be those relying on welfare payments to make ends meet who should be subject to the conditions of such a policy, he said.
"If you gave me the opportunity, should we be doing that for other people in the country who are on the other end of the scale, like maybe high income earners who don't immunise their children? Why not? Why not have a similar system based on what is important to them, [like an] income tax?" he suggested.
Dr O'Sullivan dismissed accusations of a Nanny State culture levelled at the Australian policy, saying: "Sometimes we need to acknowledge that we need to be bold and provide leadership for our citizens and .... say this is a decision we need to either make for you, encourage you, or compel you to make."
He added: "I would say any strategy that would increase immunisation, particularly among vulnerable children, is a positive one."
On Sunday Mr Abbott and his social services minister, Scott Morrison, announced that from next year people who claimed to be "conscientious objectors" to vaccination would no longer receive a childcare benefit, childcare rebate and a type of the family tax.
Current exemptions on medical or religious grounds would continue under the new policy, but religious objections would only exist where the parent was affiliated with a religious group, with a formally registered objection which had been approved by the government.
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FACTBOX:
* In Australia, 91 per cent of children are fully immunised by the age of 2.
* More than 39,000 Australian children aged under 7 are not vaccinated because of their parents' objections - an increase of 24,000 over the past decade.
* The 'no jab, no pay' policy is estimated to cost parents who refuse to vaccinate their children more than A$15,000 ($15,255) a year per child.
* 94 per cent of New Zealand children are vaccinated by the age of 2. The Government's target is 95 per cent.
* Child vaccines are free in New Zealand, and begin when your child is 6-weeks-old.
* Immunisation uses the body's natural defence mechanism, the immune response, to build resistance to specific infections.
* If you have questions, talk to your doctor or practice nurse or call the Immunisation Advisory Centre free helpline 0800 466 863.