Experts found 70 of six to 12-year-olds are given too little by GPs. Sick children recover more slowly if given too small a dose. Bugs that are not killed become immune to the drug, so they will not be wiped out by the same pills a second time.
Sonia Saxena, a GP at Imperial College London who co-authored the report, said: "It is important to understand why GPs are prescribing sub-therapeutic levels of penicillin.
"Some may be erring on the side of caution, prescribing low doses to avoid errors or side-effects.
"In the majority of cases children will still get better but under-treating those youngsters who do need antibiotics could mean more infectious complications."
England's chief medical officer has previously warned that the danger posed by growing resistance to antibiotics should be ranked along with terrorism on a list of threats to the nation.
Prof Dame Sally Davies has described it as a 'ticking time-bomb'.
She said routine operations could become deadly in just 20 years if children lose the ability to fight infection.
The authors of the study of 65,000 prescriptions to children said a review is needed because children are getting heavier and may need larger doses.