The Muslim Council of Britain ruled the treatment forbidden by Islam after parents were told the vaccine contained gelatin - which derives from pigs and is considered unclean.
Public health officials have expressed concerns over the number of Muslim children expected to be withdrawn from a national programme set to start in schools next month.
For the first time, every healthy children between the ages of two and 10 in England will be offered the Fluenz nasal spray vaccine.
An injectable alternative without gelatin does exist, but it is only offered to kids who are at a higher risk of contracting the flu.
Community leaders revealed in some areas that the "mast majority" of Muslim parents have vowed to pull their kid from the programme.
The Royal College of Public Health said the situation "added to the risk of major flu outbreaks".
Last night they urged the Government to offer a halal alternative vaccine acceptable to Muslims.
'IT'S NOT HALAL'
The spray nasal vaccine has been available since 2013 and has gradually been introduced to healthy nursery-aged kids.
The programme has led to a reduction in flu cases.
There is concern that uptake in some Muslim communities has been "significantly lower" than the average, and the most common reason for refusal given by parents being "vaccine contains porcine gelatin", according to Public Health England documents seen by The Daily Telegraph.
NHS England has urged Muslim parents to make the exception because the vaccine could be "considered different from ingesting food".
However, Dr Shuja Shafi, the chairman of the Muslim Council of Britain's research committee, said: "We have consulted the scholars and this is their view...we need another vaccine which is halal."
Comment: UK government to give flu vaccine to children under the age of nine - even though similar program failed to prevent the recent flu crisis