Many infants suffer minor reactions to the series of injections they are given at two, three or four months.
These include swelling, redness and tenderness near the injection site.
However, researchers from the Oxford Vaccine Group at John Radcliffe Hospital, found that babies given the same vaccinations using syringes with different length needles suffered very different reaction rates.
On average, for every five infants vaccinated, use of the longer needle instead of the shorter one would prevent one infant from experiencing any local reaction.
The research team wants manufacturers - who often supply the shorter needle in their vaccine packs - to review their policy.
'Abhorrent'
Dr Nigel Higson, from the Primary Care Virology Group, said that most GPs and practice nurses chose the longer needle - in preference to the shorter one for vaccinating infants.
He said: "I personally would find it abhorrent to use a shorter needle for an infant vaccination.
"What's important is to guarantee that the needle reaches the muscle, where the vaccine should be delivered.
"Obviously the longer needle is more suitable for that purpose."
He also said that thinner needles would be more acceptable for childhood immunisation.
The Oxford researchers said that the more pain and discomfort a child experienced following an injection, the less likely the parents would be to bring them back for subsequent vaccinations.
The research was reported in the British Medical Journal.