The DH's Joint Committee on Vaccination and Immunisation (JCVI) said it could not yet recommend routine infant or adolescent vaccination with Bexsero, the only currently available vaccine against meningitis B.
There were 613 confirmed cases of meningitis B in 2011/12, and 33 people died from the disease. One in ten survivors develop a major disability from the infection.
The JCVI's interim position statement said: 'On the basis of the available evidence, routine infant or toddler immunisation using Bexsero is highly unlikely to be cost effective at any vaccine price based on the accepted threshold for cost effectiveness used in the UK and could not be recommended.'
Although adolescent vaccination may be cost-effective, current evidence is insufficient to support its use, the committee said.
Bexsero was approved by the European Medicines Agency in January 2013 and is the only authorised vaccine against the disease.
The JCVI had reviewed evidence for efficacy, safety and cost-effectiveness of the vaccine using data from manufacturer Novartis, UK health protection organisations and other experts.
Professor David Salisbury, DH director of immunisation, said: 'This is a very difficult situation where we have a new vaccine against meningitis B but we lack important evidence.
'We need to know how well it will protect, how long it will protect and if it will stop the bacteria from spreading from person to person. We need to work with the scientific community and the manufacturer to find ways to resolve these uncertainties so that we can come to a clear answer.'
A spokesman for Novartis said it was 'disappointed' by the decision and that it would provide further information on pricing to the JCVI ahead of the final verdict.