WASHINGTON — For the first time ever, the Health and Human Services secretary publicly overruled the Food and Drug Administration, refusing Wednesday to allow emergency contraceptives to be sold over the counter, including to young teenagers. The decision avoided what could have been a bruising political battle over parental control and contraception during a presidential election season.

The contraceptive pill, called Plan B One-Step, has been available without a prescription to women 17 and older, but those 16 and younger have needed a prescription — and they still will because of the decision by the health secretary, Kathleen Sebelius. If taken soon after unprotected sex, the pill halves the chances of a pregnancy.

Although Ms. Sebelius had the legal authority to overrule the F.D.A., no health secretary had ever publicly done so, an F.D.A. spokeswoman said. Nor had such a disagreement been the subject of such extraordinary dueling press statements. Dr. Margaret Hamburg, the F.D.A.’s commissioner, issued a lengthy statement saying it was safe to sell Plan B over the counter, while Ms. Sebelius countered that the drug’s manufacturer had failed to study whether girls as young as 11 years old could safely use Plan B.

Ms. Sebelius’s decision on an emotional issue that touches on parental involvement in birth control for teenage children is likely to have powerful political reverberations. Scientists and politicians have been at odds for years over whether to make Plan B available over the counter. The Bush administration at first rejected over-the-counter availability for women of any age, but ultimately allowed it for women 18 and older. After a federal court order, the Obama administration lowered the age to 17 in 2009.