Children have been unable to get immunised against flu this winter because GP surgeries and schools have been hit by shortages of the nasal spray version of the vaccine that is meant to protect every two- to 11-year-old.

Supply problems have forced GP practices and primary schools in England to cancel sessions in recent weeks at which children were due to be vaccinated.

Children and young people whose health could be at particular risk if they got flu, such as asthmatics and those with a heart problem or cystic fibrosis, are among those affected.

AstraZeneca, which makes the nasal spray, admitted delays were occuring. It blamed the hold-up on the World Health Organization taking a month longer then planned to analyse the recent winter flu season in the southern hemisphere and then tell vaccine manufacturers what strains of flu to protect against in their products being deployed in Britain.

The vaccine is being offered to all primary school pupils in England, all children aged two and three as well as anyone up to the age of 17 with an underlying illness.

Parents have been left anxious that their children have not been able to get the nasal spray, known as Fluenz or LAIV, which means live attenuated influenza vaccine.

A patient at the Victoria Medical Centre in south-west London said: “My 11-year-old daughter has asthma and so must have the flu vaccine. But my doctor’s surgery has cancelled two flu clinics because of vaccine shortages and have no idea when they’re going to get new supplies.

“The government said earlier that all children aged two to 11 will be offered the nasal spray vaccine in the coming weeks. This is clearly not happening, putting children at risk from what can be a deadly disease.”

The girl’s mother added: “Flu is scary if your child has asthma.”

On Thursday 4 October, Home Farm primary school in Colchester, Essex, had to cancel plans to immunise pupils the following Monday. In an email to parents, the headteacher said it was because of a national shortage of the vaccine. It will now issue the nasal spray on 5 and 8 November.

Prof Helen Stokes-Lampard, the chair of the Royal College of GPs, said the delay was “concerning” and could damage trust in the vaccination programme.

“We have been made aware of a delay to some of the nasal vaccines that are given to children, but we have been assured that this delay will be short and that GP practices will still receive their vaccinations early enough in the season for patients to receive full benefit from them,” she said.

“We would urge parents of children not to be deterred from making arrangements for their child to get their vaccinations. But it might be worth checking that the vaccinations have definitely arrived when you book your appointment.”

AstraZeneca sought to reassure parents that sufficient quantities of the vaccine would eventually be available, so no child would miss out.

It said: “Due to the delay in strain recommendation and subsequent manufacture of new strains for the 2019-20 season, deliveries of the vaccine will be spread across the season, as opposed to being concentrated in the initial months of the season.

“AstraZeneca is manufacturing and delivering the full quantity of vaccine required for the UK childhood influenza vaccination programme.”

Public Health England said it had advised GP surgeries not to schedule sessions at which the nasal spray would be administered until mid-October.

Dr Mary Ramsay, PHE’s head of immunisation, said: “GPs have ordered supplies for adults from manufacturers in the usual way and batches of the vaccines for schools are being delivered, too. Timings for the delivery of flu vaccine are always subject to change because of the nature of the manufacturing and regulatory release processes.

“The delay in WHO announcing the strain means that we have received vaccines for children slightly later than usual and so we have been prioritising schools as they are already planning their vaccination sessions.” GPs would be able to start ordering supplies shortly, she added.

Problems have also limited the supply of the version of the flu vaccine given to 16- to 65-year-olds.