The Justice Department said it would challenge U.S. District Judge Edward Korman's early April decision that ordered the government to make the emergency-conception pills available without a prescription for girls and women of all ages.
Korman's order is to go into effect Sunday.
The Justice Department said it would ask Korman's court, the U.S. District Court of the Eastern District of New York, to stay his order until the appeal is decided.
The department said it would argue Korman had no authority to order the Food and Drug Administration to take any kind of action, saying if he had an issue he should have sent the matter back to the FDA for further action.
"The Court's Order interferes with and thereby undermines the regulatory procedures governing FDA's drug approval process," the department said in a statement late Wednesday.
The department's position was applauded by conservative, anti-abortion groups who do not want contraceptives made available to young girls.
But it was criticized by advocates for women's reproductive health and abortion rights who cite years of scientific research saying the drug is safe and effective for all ages.
"Age barriers to emergency contraception are not supported by science, and they should be eliminated," Planned Parenthood Federation of America President Cecile Richards said in a statement.
Center for Reproductive Rights President Nancy Northup said her group was "deeply disappointed that just days after President Obama proclaimed his commitment to women's reproductive rights, his administration has decided once again to deprive women of their right to obtain emergency contraception without unjustified and burdensome restrictions."
The case stems from a December 2011 decision by Secretary of Health and Human Services Kathleen Sebelius that blocked the sale of the drug to young girls without a prescription.
Sebelius said there was not enough data to prove it would be safe for girls as young as 12.
Her decision overruled the FDA, an HHS agency, which had concluded the pill was safe for over-the-counter use among girls and women of all ages without consulting a physician and decided to lift all age restrictions.
Korman, appointed to the bench by President Ronald Reagan, said April 5 Sebelius' decision was "politically motivated, scientifically unjustified and contrary to agency precedent."
He ordered the federal government to reverse its position and make the contraceptive widely available. He also gave the administration 30 days to appeal his decision.
The legal battle came a day after the FDA said a particular morning-after pill, Plan B One-Step, would now be made available without a prescription for girls as young as 15. Until the ruling, girls had to be 17 or older to buy the drug.
The Justice Department's action will not affect the FDA's Plan B One-Step decision, which went into effect immediately.
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