Mr Justice Sumner’s decision came on the same day as doctors called for the UK’s chief medical officers to resign over a target payment system for MMR vaccinations.

The GPs at a British Medical Association conference in London said the triple Measles, Mumps and Rubella (MMR) jab was the safest and best way to protect children.

But they condemned the Government for failing to convince parents about the safety of the jab.

Some parents fear the MMR vaccine could be linked to autism even though doctors and most experts say there is no evidence of a link.

In the High Court today Mr Justice Sumner ruled on two separate cases heard in private in which the fathers wanted immunisation for their daughters.

However the girls, aged four and 10, lived with their mothers who felt vaccinations involved unacceptable risks and, if imposed, would cause them great distress.

Mr Justice Sumner said the benefits of having the MMR jab outweighed any risks.

"Recognising the anxieties of the mothers, and that an adverse decision will be upsetting, the children’s best interests are served by receiving a programme of immunisations and an order should be made," he said.

The judge said he accepted a parent had a right to choose whether or not to accept medical advice on immunisations.

But in this case the parents did not agree and he had been persuaded by the evidence from leading doctors that immunisation was in the best interests of the girls.

He said the mothers were devoted to their children and had taken a stand on what they felt was best for their daughters, who were identified only by the initials C and F.

The fathers acknowledged the risks but had said their views were supported by current medical research and thinking.

As well as MMR, the judge ordered the girls should be immunised against other diseases including diphtheria, tetanus, whooping cough and meningitis.

Meanwhile, GPs attending a British Medical Association (BMA) conference in London today called for the UK’s four chief medical officers to resign.

Chichester GP Dr Grant Kelly said they should take the blame for the payment system, under which GPs who fall short of immunisation targets lose money.

Dr Jeffrey Moysey, a GP from the West Pennine area, said the present Government prided itself on spin and presentation but had failed to persuade the public about the safety of MMR or provide a creditable alternative.

He said the payment system meant patients felt doctors had a vested interest in reporting MMR.

"All of us believe that the take up of MMR should never be linked to practice income," he said.

The Local Medical Committees conference voted in favour of calling on the CMOs to resign.

The decision is likely to be adopted by the BMA’s GP Committee but this does not make it official policy for the whole BMA.

A spokesman on behalf of all UK departments of health said the conference decision did not relate to the effectiveness and safety of MMR, which doctors fully endorsed.

He said a sudden change in the current target payments would not have a predictable effect on vaccine uptake levels. "However, the chief medical officers have met individually with general practitioner leaders on several occasions and indicated their willingness to discuss using the target payments more effectively, in a way that meets GP concerns and encourages even higher uptake levels, protecting children from potential life-threatening diseases," he said.