In some areas the 'vast majority' of Muslim parents have vowed to withdraw their children from the programme, community leaders revealed.
Tonight the Royal Society for Public Health said the situation 'added to the risk of major flu outbreaks' and urged the government to offer a halal alternative vaccine acceptable to Muslims.
Since 2013 the nasal spray vaccine has been gradually introduced to healthy children, beginning with youngsters in nursery school. An injectable alternative without gelatine does exist, but is only offered to children at higher risk.
The programme has resulted in a significant reduction in flu cases, and from August the Fluenz spray will be offered to every child between the ages of two and ten.