The Obama administration stunned women’s health advocates and abortion opponents alike Wednesday by rejecting a request to let anyone of any age buy the controversial morning-after pill Plan B directly off drugstore and supermarket shelves.

For what the Food and Drug Administration thinks is the first time, the Department of Health and Human Services overruled the agency, vetoing the FDA’s decision to make the contraceptive available without any restrictions. Revealing a rare public split, FDA Administrator Margaret A. Hamburg said her conclusion that the drug could be used safely by women of all ages was nullified by Health and Human Services Secretary Kathleen Sebelius.

“There is adequate and reasonable, well-supported, and science-based evidence that Plan B One-Step is safe and effective and should be approved for nonprescription use for all females of child-bearing potential,” Hamburg said in a statement.

“However, this morning I received a memorandum from the Secretary of Health and Human Services invoking her authority under the Federal Food, Drug, and Cosmetic Act to execute its provisions and stating that she does not agree with the Agency’s decision.”

In a statement and separate letter to Hamburg, Sebelius said she reversed the FDA’s decision because she had concluded that data submitted by the drug’s maker did not “conclusively establish” that Plan B could be used safely by the youngest girls.

“About ten percent of girls are physically capable of bearing children by 11.1 years of age. It is common knowledge that there are significant cognitive and behavioral differences between older adolescent girls and the youngest girls of reproductive age,” Sebelius said.

Her action means that instead of being able to pick up Plan B off store shelves, like condoms and spermicides, girls 16 and younger still need a doctor’s prescription to obtain it. Women 17 and older can buy the pill without a prescription but must show proof of age to a pharmacist.

The decision shocked and angered the doctors, health advocates, family-planning activists, lawmakers and others who supported relaxing the restrictions to help women, including teenagers, prevent unwanted pregnancies.

“We are outraged that this administration has let politics trump science,” said Kirsten Moore of the Reproductive Health Technologies Project, a Washington-based advocacy group. “This administration is unwilling to stand up to any controversy and do the right thing for women’s health. That’s shameful.”

Susan F. Wood of George Washington University, who resigned from the FDA in 2005 because of delays by the George W. Bush administration in relaxing restrictions on Plan B, said she was “beyond stunned” by the decision.

“There is no rationale that can justify HHS reaching in and overturning the FDA on the decision about this safe and effective contraception,” Wood said. “I never thought I’d see this happen again.”

Opponents of easier access, meanwhile, hailed the decision, saying relaxing the rules would have exposed girls and women to risks from taking high doses of a potent hormone and misusing the medication; interfered with parents’ ability to monitor their children; and made it easier for men to prey on vulnerable minors.

“Plan B can act in a way that can destroy life,” said Jeanne Monahan of the Family Research Council, a conservative advocacy group. “A decision to make Plan B available for girls under the age of 17 without a prescription would not have been in the interest of young women’s health.”

A long controversy

Plan B has long been controversial and was the focus of one of the most contentious health disputes during the Bush administration. It works primarily by preventing an egg from being fertilized. But critics focus on the chance that it might prevent a very early embryo from implanting in the womb, an action they consider equivalent to an abortion. As a result, some doctors refuse to write prescriptions for it, some pharmacists refuse to fill requests, and some hospitals refuse to provide it to patients.

Wednesday’s decision came as the administration is trying to defuse rising tensions with the Catholic Church over several issues, including a proposed mandate that private insurers provide women with contraceptives for free and a federal denial of an anti-human-trafficking grant to the U.S. Conference of Catholic Bishops.

“I welcome the . . . decision not to expand nonprescription use of Plan B to all minors of childbearing age,” said the conference’s Deirdre McQuade. Plan B “could endanger the lives of newly conceived children through its abortifacient action, put minors at risk for unnecessary side effects, undermine parental rights and contribute to higher STD [sexually transmitted disease] rates.”

A senior White House official, who spoke on the condition of anonymity to freely discuss the internal process, said the decision rested entirely with Sebelius, who informed the White House of her conclusion ahead of time. The administration trusted her on both the substance and politics of the issue, the official said, noting that Sebelius had been governor of Kansas, a conservative state that required deft decision-making by a Democratic governor.

A Health and Human Services spokesperson said in an e-mail that the “decision was based on a careful consideration of the science.”

President Obama pledged in 2009 to prevent politics from interfering with scientific decisions. The Bush administration had been accused of censoring federal scientists on climate change and other hot-button issues.

But Wednesday’s decision was not the first time the Obama administration has overruled the scientific advice of senior officials. In September, Obama pulled back smog standards proposed by Environmental Protection Agency Administrator Lisa P. Jackson, saying they would impose too heavy an economic burden.

The administration has long tried to find common ground on issues related to abortion and birth control. The White House hosted meetings aimed at finding areas of agreement among activists, but the effort foundered. In 2010, the administration tried to appease both sides in the debate over sex education and abstinence, launching a campaign supporting programs of both types.

Rules gradually relaxed

The Plan B request followed a series of steps that have gradually made the emergency contraceptive easier to obtain.

The drug contains a higher dose of a synthetic form of the hormone progesterone than is found in many standard birth-control pills. It was approved in 1999, but only for women who obtained a prescription from a doctor. Taken within 72 hours of unprotected sex, the pill has been shown to be 89 percent effective at safely preventing pregnancy.

In 2003, Plan B’s maker asked the FDA to allow the contraceptive to be sold without a prescription so women would not have to scramble — often in late-night or weekend panics after sex without protection, a failed condom or a rape — to find both a doctor to write a prescription and an open pharmacy.

The FDA delayed a decision on that request for three years, ignoring recommendations by outside advisers and internal reviewers. It approved nonprescription sales in 2006, but only to women age 18 and older.

In 2009, the agency allowed the sale of Plan B One-Step, a new version that works with one pill instead of the original two, to 17-year-olds without a prescription. But the decision came only after a federal judge ordered the change in response to a lawsuit.

In February, the drug’s maker, Teva Pharmaceutical Industries, asked the FDA to drop the remaining restriction, citing two new studies that it said showed that girls as young as 11 could use the product properly and safely.

A hearing is scheduled for Tuesday on a motion to declare the FDA in contempt of court for failing to review earlier its decision to leave age restrictions in place.

Another morning-after pill, Next Choice, the generic version of the original two-pill Plan B that sells for about $35, is available only by prescription.

Staff writers N.C. Aizenman, Juliet Eilperin and Anne Kornblut contributed to this report.