The family, including the boy's mother who was diagnosed with hepatitis B several years ago, went on the run after a court ordered them to vaccinate the newborn against the disease that can lead to liver cancer and cirrhosis, according to the Sydney Morning Herald.
"We gathered some things and fled the house," the unidentified father, a financial adviser, told the paper after leaving his Sydney home.
"I don't agree with the one-size-fits-all policy. He is a small baby (2.49 kilograms) and they give the same dose to babies twice his size. I just wanted time to get more information about the vaccine."
The baby's father and Chinese-born mother went into hiding Friday when child protection authorities won a state Supreme Court order after the couple refused to have their son vaccinated following his birth in a Sydney hospital.
The couple believe aluminium in the vaccine could cause him more damage than contracting hepatitis B. They feel the disease could be more effectively managed than any potential neurological damage they fear the child might contract from the vaccine, they told the Herald,
While vaccinations are not compulsory in Australia, New South Wales state health policy mandates that parents of all babies born to hepatitis-B-positive mothers must be offered immunoglobulin for the child within 12 hours of birth and four doses of the vaccine over six months.
When the father failed to show up for a doctor's appointment to find out more about the risks of vaccinations, he was told the child would be taken from him for vaccination, prompting the family to flee, he told the paper.
He also admitted that he had refused to have his daughter vaccinated against hepatitis B when she was born in 2005.
One of the doctors who alerted state authorities to the couple's refusal to have the baby vaccinated said the child's rights were being ignored.
"I am a strong believer in vaccinations being voluntary but not getting this baby vaccinated is a form of child abuse," said David Isaacs, a professor in paediatric infectious diseases.
"We are talking a potentially major and awful outcome for this child and it is our job to protect children when they can't make decisions for themselves," the Herald quoted him as saying.