A judge has ordered a mother and father take their newborn baby to hospital for urgent hepatitis B injections, despite the parents’ opposition to vaccinations.

Brisbane Supreme Court Justice Jean Dalton made the order last year – but only published her reasons today – after doctors made an urgent application to give the child two preventative vaccines.

During the application the court heard the baby, which was just 40 hours old at the time, had a 20 per cent chance of being infected with the virus, of which the mother has a chronic form.

If the baby was infected, it was almost certain to develop a chronic infection and would be at risk of cancer and liver disease.

The parents opposed the application on the grounds they did not agree with vaccination because of religious beliefs.

The father also had philosophical concerns about the financial agendas of pharmaceutical companies in distributing these drugs, the court heard.

The parents argued the percentage chance of the baby being infected was low enough to risk not giving it the injections, which had to be delivered within 48 hours of birth.

However Justice Dalton said that the immediate welfare of the child outweighed the parents’ concerns, and ordered they take the baby to hospital immediately.

Justice Dalton refused to make orders about a future vaccination schedule for the virus, advising the parents to seek legal assistance if they wished to continue their dispute against treatment.

AAP