The government has hailed the new pneumococcal vaccination (PCV) a success following a dramatic decline in the number of pneumococcal disease cases, including meningitis and septicaemia.
However, the Health Protection Agency (HPA) says that 12% of children are still open to the diseases by not taking the jab.
The HPA estimate that 300 children have avoided illness by taking the vaccination.
Sue Davie, Chief Executive at the Meningitis Trust, said: "Pneumococcal meningitis is a devastating disease and vaccination is the only way to prevent it. That means it is important for parents to immunise their children.”
The vaccine was introduced in September last year.
Health minister Ben Bradshaw said: ‘Vaccinating children against harmful diseases is one of the easiest and most important health measures we can take. These figures are a stark reminder of the importance and benefits of immunisation.’