A vegan mother who wanted her sons to live a "toxin free" life will be forced to make them receive routine vaccinations after the High Court overruled her objections.

"I am truly sorry that the mother will regard the decision as wrong, but my objective duty is clear," Judge Mark Rogers said, before ordering that the boys, aged two and four, be given injections against diseases including diphtheria, polio, meningitis, measles, mumps and rubella.

The mother had said that she feeds her children only “natural products”.

She said: “Their bodies are as free of toxins as I can possibly make them."

The older of the boys had had some vaccinations, but the mother told the court she believes he has suffered side effects including cradle cap, a persistent cough and eczema as a result.

But the boys’ father told the court their mother is “obsessive, over-protective and narrow-minded” and has “a suspicion of all conventional medicine” and does not allow them to have paracetamol-based medication designed for children like Calpol.

The mother, who cannot be named to protect the anonymity of the children, told the court: “What I have learned is that yes, vaccines do work some of the time, but there is a definite risk with vaccination. The vaccine manufacturers have cited that vaccines are ‘unavoidably unsafe.' There is a very rare risk that either of the children will ever catch one of the diseases listed in this report. Both children have strong immune systems which definitely helps in protecting them from diseases.”

Speaking of her ethical beliefs, she said: “No vaccine is vegan. No doctor will criticise the action of a vaccination or they will be afraid of losing their job. It is not natural to be injected with metal elements and a vegan it goes against my beliefs for my child to be injected with something that is grown on animal cells or something that has been tested on animals.”

Judge Mark Rogers said the mother had been unable to get a doctor to appear in court to support her views and ruled in favour of the father, meaning the boys will receive routine vaccinations for measles, mumps and rubella as well as diphtheria and polio.

The judge said in his ruling published yesterday: “I have serious concerns as to (the mother’s) ability to look objectively and even-handedly.”

He upheld the decision that the children should be vaccinated under the terms of the 1989 Children’s Act, which allows courts to overrule a parent for the welfare of the child.

A test case in 2013 at the High Court found that two sisters aged 11 and 15 should be given the MMR vaccine even though they and their mother did not want them to have it.

In 1998, a study by Dr Andrew Wakefield published in respected medical journal The Lancet suggested the MMR jab could be linked to autism and bowel disease.

The report and the media frenzy that followed prompted many parents to decide against having their children vaccinated with the three-in-one injection.