A vaccine containing mercury given to babies when they are eight weeks old is to be scrapped amid fears of a link with autism.
The whooping cough vaccine contains mercury
The move follows recent research in America that suggests a connection between the mercury used to preserve the whooping cough vaccine, and autism.
The jab, without mercury, will be given as part of a new five-in-one vaccine.
The Department of Health has always maintained there is no evidence of such a link.
Doctors are also being told to switch from the live polio vaccine, currently given by mouth, to a "killed" vaccine injection to avoid rare cases of polio contamination, according to a report in The Daily Telegraph newspaper.
GP Richard Halverson welcomed the "long overdue" changes.
He told BBC News: "I welcome the fact that mercury is being withdrawn because it is toxic and should not be injected into babies full stop.
"Mercury is one of the most toxic elements on this planet. It has no business
being ingested in any form by anyone, it serves no useful purpose, it is
He also welcomed changes to the polio vaccine, saying it was "disgraceful" that the only cases of paralysis from polio in the UK in the last 15 years had been as a result of the vaccine.
Health Minister John Hutton has confirmed the changes to childhood vaccines.
"Childhood immunisation has been extremely effective in protecting children from serious life-threatening diseases", he said in a statement.
"We are continually looking at ways to improve this programme as new, more effective products become available."
He said the new five-in-one injection, containing vaccinations for diphtheria, tetanus, whooping cough, hib and polio, would be introduced later in the year.
The UK's leading autism charity, the National Autistic Society, welcomed the removal of mercury from vaccines.
A spokeswoman said the society had always "supported moves to ensure that mercury is not used within the immunisation programme as a precautionary measure".
But Jackie Fletcher, founder of the parent support group Justice, Awareness and Basic Support, said that, while supporting the removal of mercury, she was "extremely worried" about plans for the replacement five-in-one jab.
She said: "With five-in-one vaccines we would want to know what safety trials have
taken place. How did they find out it was safe to do it in this combination?
"We know that for other vaccines the safety trials have been extremely
Increasing the combinations increased the potential for an adverse reaction, she said.
"What we want to see is more choice, where the vaccines are designed around what is right for the individual child."
In June, it was announced that US researchers at Columbia University found autism-like damage in the brains of mice exposed to thiomersal, the preservative used in the whooping cough vaccine.
Despite other US and European studies finding no link between mercury and autism, the Columbia team said they found that mice exposed to thiomersal showed signs of changed behaviour, and brain abnormalities.
The animals had been bred to be vulnerable to developing disorders of the immune system.
The study team argued it was possible that children with similarly-compromised immunity may also be at risk.