The UK’s Medical Defence Union said it knew of a handful of recent cases in which children were given flu vaccines unsuitable for their age group.
Some of the jabs in the seasonal flu vaccine programme are not licensed for children under four.
Already “excellent” programme delivery would be improved by reducing errors, the Department of Health (DoH) said.
A spokeswoman for the department said: “It is the responsibility of the doctor or nurse giving the vaccine to check and ensure it is the right vaccine for the patient.”
Last year the DoH published a warning against using some flu vaccines after reports that some youngsters had suffered febrile convulsions following the jab.
Officials said it was important that youngsters aged over six months in at-risk groups – such as asthma sufferers or those with a compromised immune system – received the vaccine, but care should be taken to use the right one.
It warned against giving the jabs Enzira or CSL Biotherapies generic influenza vaccine, marketed by Pfizer, to children under five.
In the last five years the MDU said it had received 108 reports of errors in immunising children using all types of jab, including against meningitis.
In a statement, it said: “The MDU has received a number of calls from members on its advice line recently where there has been a mix-up over the type of vaccine administered to children.
“In addition, a survey of cases reported to the MDU has revealed that 108 immunisation errors were reported over the last five years.
“Of these, 98 (90%) involved children and three concerned doctors administering the incorrect seasonal influenza vaccine to children.”
MDU medico-legal adviser Dr Jacqui Phillips said that although the number of adverse incidents is low considering the numbers of immunisations given, “vaccine errors do represent a sizeable proportion of the medication incidents notified to the MDU”.
“Not all seasonal flu vaccines are suitable for children and GPs need to ensure that neither they nor practice staff administer the incorrect ones,” she said.
The MDU recommends doctors and practice nurses thoroughly check records prior to administering a vaccine.