The Family Court is expected to side with a father who wants his child vaccinated, rather than her mother who doesn't.

The father of the girl - who was soon to start school - wanted her to get her shots, in line with Ministry of Health and World Health Organisation guidelines.

But the mother, who is strongly anti-vaccination, felt her daughter is at risk of an adverse reaction to immunisation thanks to "a strong personal and family history for dairy and gluten intolerance, eczema, food and chemical sensitivities and medication-adverse reactions".

The father filed an application in January 2018 under the Care of Children Act 2004 with a two-page affidavit outlining his reasoning. That October, the mother filed a 33 page affidavit in response, along with 150 pages of evidence.

These included a letter from the girl's GP, the results of genetic testing done by a naturopath, and "information obtained from her own research on the internet".

She also included an affidavit from Canadian professor Dr Christopher Shaw, who is well known for his anti-vaxx views.

The mother had sought to file evidence from another two US-based doctors, one of whom said the girl was at risk of allergic reactions to chemicals in the vaccines.

A preliminary hearing was held at the Waitakere Family Court in December to decide whether that evidence is admissible.

Family lawyer Sharon Chandra told Mike Hosking the Ministry of Health has set guidelines over immunisation.

"It seems highly unlikely that the Family Court is going to go against Ministry of Health's guidelines."

She said that it would only be if there is a specific reason related to a specific child "as to perhaps an adverse reaction for a particular child or an impact of a vaccination for that child".

Chandra said that debates over vaccinations are becoming increasingly more common, but each case is judged individually rather than as a whole. 

In her decision published in June, Judge Belinda Pidwell decided neither of those doctors had adequate knowledge of the New Zealand immunisation programme, neither had examined the girl directly and neither was fully credible.

Given the Court had already ordered a report from a New Zealand expert, she declined the mother's application to file additional evidence.

The judge said it was important to determine what was in the child's best interest, pointing out there was "a heightened risk to her, and other school children, whilst the issue remains undetermined. [She] poses a risk to other children whilst she is unimmunised, and she is susceptible to a range of illnesses".

The Court has not yet made a decision on whether the girl should be immunised.