A US anti-vax mother is locked in a bitter legal battle over her teenage daughter's right to remain unvaccinated, claiming their school had violated their "religious beliefs".

She is claiming she is being religiously persecuted for not vaccinating her two daughters, aged 13 and 15.

The girls' upstate New York high school has refused to teach either of them for the past two months after it emerged that their vaccinations weren't up-to-date and their mother wouldn't give her permission.

The girls' mother, Marina Williams, claimed they had always been given a "religious exemption" to immunisation programs in the past.

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She has since sued the school for refusing to educate her girls, claiming the school's leaders are breaking the law.

The Williams family belong to a religion known as the Temple of the Inner Flame Church.

There is very little evidence online to corroborate the existence of this religion but Ms Williams claims it is a major part of her life.

Local television station WIVB reports that one of the religion's rules prohibit followers from putting foreign substances like drugs, alcohol and vaccines in their bodies.

It's a rule Ms Williams and her family strictly adhere to, even though it's not known if her daughters are believers as well.

"I've never had a vaccine before. My mother, my sister, my aunt, my grandmother haven't either," she said. "To me, that was just a given … it's not something I've ever had to defend before."

According to WIVB the school district denied Ms Williams' application for a religious exemption, so she took her complaint higher, to the Board of Education.

This too was denied, forcing Ms Williams to engage a solicitor to appeal to the Commissioner of Education, an undertaking that could take months.

In the meantime, Ms Williams said her two daughters are "falling behind" in their school year.

Frank Housh told the television station that his client's children are not legally required to be vaccinated, but they are legally required to be educated.

"We understand that there are large public health concerns related to vaccination, but that is not what this case is about," he said.

"These children don't have to be vaccinated if they have a legitimate religious reason not to do that. The law says they have to be educated, they (the school) are refusing to do that."

According to Ms Williams, her religious freedom is being violated by school district, which is against the law.

"It's religious persecution for the most part and that's not OK with me," she said.

"The Orchard Park school system is asking me to go against everything that I believe in and my faith."