But in doing so, at least one opponent of easy access to the contraception thinks the president is buckling to political pressure, rather than making the health of girls a priority.
The Justice Department notified U.S. District Judge Edward Korman on Monday that it will submit a plan for compliance. If he approves it, the department will drop its appeal of his April ruling.
According to the department's letter to the judge, the Food and Drug Administration has told the maker of the pills to submit a new drug application with proposed labeling that would permit it to be sold "without a prescription and without age or point-of-sale prescriptions." The FDA said that once it receives the application, it "intends to approve it promptly."
Advocates for girls' and women's rights said the federal government's decision to comply with the judge's ruling could be a move forward for "reproductive justice" if the FDA acts quickly and puts emergency contraception over the counter without restriction.
"It's about time that the administration stopped opposing women having access to safe and effective birth control," Annie Tummino, coordinator of the National Women's Liberation and lead plaintiff in a lawsuit over unrestricted access to the morning-after pill, said in an emailed statement.
She said women and girls should have "the absolute right to control our bodies without having to ask a doctor or a pharmacist for permission."
NARAL Pro-Choice America President Ilyse Hogue welcomed the decision by the Obama administration.
"By making emergency contraception available to women of all ages, the FDA is taking an important step to reduce unintended pregnancies and put women in control of their futures," Hogue said in a statement.
But an opponent of the contraception plan, at the anti-abortion Family Research Council, criticized the government for not sticking with its decision to appeal.
"We're very concerned and disappointed at the same time because what we see here is the government caving to political pressure instead of putting first the health and safety of girls (and) parental rights," said Anna Higgins, director of the council's Center for Human Dignity.
The government had appealed the judge's underlying April 5 ruling, which ordered emergency contraceptives based on the hormone levonorgestrel be made available without a prescription, over the counter and without point-of-sale or age restrictions.
It had asked the judge to suspend the effect of that ruling until the appeals court could decide the case. But the judge declined, saying the government's decision to restrict sales of the morning-after pill was "politically motivated, scientifically unjustified and contrary to agency precedent." He also said there was no basis to deny the request to make the drugs widely available.
The government had argued that "substantial market confusion" could result if the judge's ruling were enforced while appeals were pending, only to be later overturned.
Last week, an appeals court dealt the government a setback by saying it would immediately permit unrestricted sales of the two-pill version of the emergency contraception until the appeal was decided.
The morning-after pill contains a higher dose of the female hormone progestin than is in regular birth control pills. Taking it within 72 hours of rape, condom failure or just forgetting regular contraception can cut the chances of pregnancy by up to 89 percent, but it works best within the first 24 hours. If a girl or woman already is pregnant, the pill, which prevents ovulation or fertilization of an egg, has no effect.
The FDA was preparing in 2011 to allow over-the-counter sales of the morning-after pill with no limits when Health and Human Services Secretary Kathleen Sebelius overruled her own scientists in an unprecedented move.
The FDA announced in late April that Plan B One-Step, the newer version of emergency contraception, the same drug but combined into one pill instead of two, could be sold without a prescription to those age 15 or older. Its maker, Teva Women's Health, plans to begin those sales soon. Sales had previously been limited to those who were at least 17.
The judge later ridiculed the FDA changes, saying they established "nonsensical rules" that favored sales of the Plan B One-Step morning-after pill and were made "to sugarcoat" the government's appeal.
He also said they placed a disproportionate burden on blacks and the poor by requiring a prescription for less expensive generic versions of the drug bought by those under age 17 and by requiring those age 17 or over to show proof-of-age identification at pharmacies. He cited studies showing that blacks with low incomes are less likely than other people to have government-issued IDs.
Reluctant to get drawn into a messy second-term spat over social issues, White House officials have argued that the FDA and the Department of Justice were acting independently of the White House in deciding how to proceed. That approach continued Monday, with the White House referring all questions about the decision to Health and Human Services.
Still, Obama has made clear in the past that he feels strongly about the limits, and he said in 2011 he supported Sebelius' decision to impose them despite the advice of her scientists.
"As the father of two daughters, I think it is important for us to make sure that we apply some common sense to various rules when it comes to over-the-counter medicine," Obama said then.