They are taken by thousands of people in Britain on a daily basis.
Tests on volunteers given the supplements during an 11-week exercise trial showed evidence of reduced mitochondrial activity in the muscles.
Mitochondria are tiny power houses in cells that generate energy by burning up calories.
"Our results show that vitamin C and E supplements blunted the endurance training-induced increase of mitochondrial proteins, which are needed to improve muscular endurance," said study leader Dr Goran Paulsen,
from the Norwegian School of Sport Sciences.
During the trial, 54 young and healthy men and women were randomly given vitamin C and E supplements or a "dummy" placebo pill.
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The daily doses were 1000 milligrams of vitamin C and 235 milligrams of vitamin E, levels typically found in supplements sold on the High Street.
Three or four endurance sessions were completed per week, mostly involving running. Fitness levels, blood samples and muscle tissue were all analysed at the start and end of the study.
The supplements had no obvious effect on participants' oxygen uptake or their performance in a 20 metre shuttle run test.
But the scientists found that molecular markers for the production of new muscle mitochondria only increased in the group not given the vitamins.
"Our results indicate that high dosages of vitamin C and E - as commonly found in supplements - should be used with caution, especially if you are undertaking endurance training," said Dr Paulsen.
"Future studies are needed to determine the underlying mechanisms of these results, but we assume that the vitamins interfered with cellular signalling and blunted expression of certain genes."
Previous studies have shown that physical exertion increases the production of oxidising "free radical" molecules which may help to trigger muscle changes.
Vitamins C and E both act as powerful antioxidants, which can have health benefits. But by reducing oxidative stress too much they may curb the body's natural response to exercise, the scientists believe.
The findings are published in the latest edition of the Journal of Physiology.