But the U.S. government is defending the mandate, saying that it is needed to ensure that all women have access to key benefits that ensure their health.
"Birth control ... is the most commonly taken drug in America by young and middle-aged women," said Secretary Kathleen Sebelius of the U.S. Department of Health and Human Services, which issued the rule. Contraceptives have health benefits for women and reduce health care costs, she said.
Moreover, she said, "this proposal strikes the appropriate balance between respecting religious freedom and increasing access to important preventive services."
The proposal is supported by women's groups and pro-choice organizations. Some Catholics also support the move.
"The bishops do not speak for us," Catholics for Choice, a liberal advocacy group, said in a statement. "In shouting ... from the pulpit, they are threatening to drown out the voice of the majority of Catholics who believe that women should be able to access birth control."
The president of the group, Jon O'Brien, said that many Catholic employers are "major business enterprises that ... get federal money" and so should offer such coverage. He said four of the 10 largest health care systems in the U.S. are Catholic.
Liberal Catholics note that 98% of Catholic women have used contraception, despite church teachings. And about half of U.S. Catholics who leave their faith cite their unhappiness with the church's teachings on birth control as a reason they left, according to a 2009 Pew survey.
Supporters also note that the rule gives an exemption for religious institutions that only serve their particular faith group. That would exempt, for example, a Catholic parish. But the exemption would not apply to institutions such as Catholic hospitals or schools, which often serve non-Catholics.
The rule has now become a hot-button issue in the presidential race as both parties try to win over the Catholic vote.
Newt Gingrich, who is Catholic, said last week that the mandate shows that the Obama administration "has declared war on the Catholic church."
Mitt Romney said Friday he would repeal the mandate his first day in office.
Some liberal Catholics and others who had supported President Barack Obama's health care plan also are upset by the rule.
Sister Carol Keehan of the Catholic Health Association said the move "jolted us."
The controversy started when Obama's health care plan was approved in 2010. Part of the plan called for coverage in all plans to ensure that women have access to medical care that meets their needs.
In August, the HHS issued an interim rule that said most health care plans will have to cover contraceptive services. The Jan. 20 ruling affirmed that earlier statement.
Part of the debate centers on what exactly is a religious employer.
The Obama administration essentially defined it as one that serves only people who belong to its faith. Such employers will be exempt from the rule. But Catholic critics say the definition should have been broadened to include religious institutions that also serve people of different faiths.
Supporters of the rule say that people who work for religious organizations should have the right to full health care coverage. They shouldn't be penalized just because their employer happens to promote a specific faith, they argue.
Most groups have until August to comply with the mandate. But religious organizations have an extra year to comply, until August 2013.
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