He said the rule "carves out a narrow exemption" and keeps the contraceptive mandate in place for those without moral or religious objections to it.
Both rules would take effect as soon as they are on display at the office of the Federal Register.
The agency calculated that at most, 120,000 women would be affected: mainly those who work at the roughly 200 entities that have been involved in 50 or so lawsuits over birth control coverage. The Trump administration was reportedly planning to roll back the birth control mandate.
"I can't imagine that many employers are going to be willing to certify that they have a moral objection to standard birth control methods", said Dan Mendelson, president of the consulting firm Avalere Health. "Today's actions affirm the Trump administration's commitment to upholding the freedoms afforded all Americans under our Constitution", the statement said.
The move could lead hundreds of thousands of women - who thanks to the ACA had their contraception fully covered by their health insurance plans - to now pay out of pocket for their birth control.
"It is basic health care the vast majority of women will use in their lifetime".
"The government already engages in dozens of programs that subsidize contraception for the low-income women", it said.
The mandate, which has been the subject of multiple legal challenges, has required employers that provide health insurance to include contraceptive coverage.
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Apparently, the Trump administration intends to enact the new laws immediately, saying "it would be impracticable and contrary to the public interest to engage in full notice and comment rule-making".
In a press call on Friday, Rienzi said such fears are unfounded.
President Donald Trump's administration Friday refuted his predecessor's insistence that religious organizations pay for contraceptives for their employees in violation of their faith, with a new proposed rule that creates an exemption for them.
The Family Policy Institute of Washington commended Trump for keeping his campaign promise on health care and the Department of Justice's issuing of a memorandum on federal laws protecting religious liberties. "They're taking contraception coverage away from women without justification".
Brown said that weakening contraception coverage could also take a toll on maternal mortality, community health and economic stability of women and families. "It prevents adolescent pregnancies".
"This appears to be a common sense, balanced rule and a great step forward for religious liberty", he said.
"Under the Obama administration, this constitutional right was seriously eroded", Ryan said in a statement, adding: " The conscience protections installed will ensure that people and organizations can freely live out their religious convictions and moral beliefs".
The Trump administration's revision broadens a religious exemption that previously applied to houses of worship, religion-affiliated nonprofit groups and closely held private companies.
The announcement from the Department of Health and Human Services reignites a fierce battle over the controversial provision.