Some schools will need to reschedule flu vaccination sessions due to take place in mid-November following supply delays, according to PHE.
PHE said GPs might have to vaccinate the children who would have normally received their flu vaccine at school.
GPs in England will be expected to vaccinate primary school children in high-risk groups following the delay to vaccination sessions in schools.
This is due to a delay in the delivery of the childhood nasal spray flu vaccines – due to arrive in November – which has affected around a quarter of the overall number of vaccines that have been ordered.
However, PHE could not confirm a new date, saying clinics will be rescheduled ‘as soon as possible’.
Priority should be given to children in at-risk groups and younger children aged two and three, PHE advised.
Pharmaceutical supplier AstraZeneca said the delay only affects certain batches of Fluenz Tetra vaccine stocks, caused by routine testing process rather than safety or efficacy issues.
PHE head of immunisation Dr Mary Ramsay said: ‘We are working with AstraZeneca and NHS England and Improvement to ensure that all eligible children get their flu vaccine as soon as possible. Children who have underlying medical conditions that make them more vulnerable to flu will be prioritised by GPs first.’
AstraZeneca country president Laurent Abuaf said: ‘We realise how important it is to deliver a full supply of vaccine to the NHS and are doing everything possible to minimise the delay of these affected batches.
‘As part of our normal product release process, we need to repeat some tests before a portion of our vaccine supply can be released and delivered. It is paramount that all batches complete the testing process before they can be supplied, and we are working as fast as possible to achieve this.
‘We are committed to working in partnership with PHE and the Department of Health and Social Care to support the earliest possible delivery of all the nasal spray vaccine needed for the NHS childhood seasonal flu immunisation programme.’
Official figures released by NHS Digital in September showed that coverage of all 13 childhood vaccinations fell over the last year.
Meanwhile, NHS Digital said it expects only 40% of practices to have the right IT systems this autumn to receive flu vaccination data electronically from community pharmacies.
This article has been changed. It initially said the delay was to the start of the programme, however this was incorrect. This began in October.