The Minister of Health says the parents who want only unvaccinated blood for their baby's heart surgery should "listen to the health advice on offer".
Te Whatu Ora is making an application under the Care of Children Act regarding the baby who needs open heart surgery.
The appeal has been sparked by two parents' refusal to use vaccinated blood in the procedure to treat their child's severe heart disease.
The health agency is asking that the baby be placed under the guardianship of the court before appointing the doctors as agents of the court for medical care, and the parents agents of the court for all other care.
Little said the parents should consider their decisions carefully and he believed the High Court application was appropriate.
"Parents should be guided by the best clinical advice going," he said.
"Sometimes these are very difficult decisions when parents have very strong values in a particular situation.
"When there is a child involved who is not capable of making decisions for themselves and on their own behalf, it is important parents think carefully of the clinical benefits of what is on offer, in the best interests of the child.
Health authorities did apply for guardianship on rare occasions when parents make decisions "not in their child's best interests," Little said.
"[It] does happen. I think we have a system in place to deal with that, it is distressing for everybody. But these are the right steps to take."
There will be a full hearing into the case next week.
World-first blood test 'ground-breaking'
Little was today at Christchurch Hospital emergency department for the launch of new technology to diagnose heart attacks more quickly.
A world first bedside blood test that could diagnose heart attacks in minutes could save the health system millions of dollars and get patients treated faster, Little said.
A research team, led by Christchurch Hospital emergency medicine specialist Dr Martin Than, has been working for a decade on finding better ways of diagnosing heart attacks.
They have developed a blood test that can be analysed at the bedside, which is as precise as a laboratory test.
The scheme is being used in other hospitals across the country, where the average stay of cardiac patients in emergency departments has been cut by three hours, saving the health system an estimated $50-$70 million.
Little dubbed the innovation "groundbreaking".
"Clearly, this is good for patients - those who can go home instead of spending hours in hospital worrying they are having heart attacks, and those who actually are having heart attacks and get the treatment they need sooner.
"But it's also good for the health system, because sending people home within an hour of arrival takes pressure off the hospital and frees an ED bed up for someone else."