Obama called for insurance companies be the ones directly responsible for providing free contraception.
"Religious liberty will be protected and a law that requires free preventative care will not discriminate against women," Obama said in a brief appearance in the White House briefing room.
Women will still get guaranteed access to birth control without co-pays or premiums no matter where they work. But religious universities and hospitals that see contraception as a violation of their faith can refuse to cover it, and insurance companies will then have to step in.
The Obama administration had announced on Jan. 20 that that religious-affiliated employers had to cover birth control free of charge as preventative care for women, and they were given an extra year to comply, until August 2013, but opponents responded with outrage.
Catholic cardinals and bishops across the country assailed the policy in Sunday Masses, and Republican leaders in Congress promised emergency legislation to overturn Obama's move.
"I understand some folks in Washington want to treat this as another political wedge issue. But it shouldn't be. I certainly never saw it that way," Obama said. "This is an issue where people of good will on both sides of the debate have been sorting through some very complicated questions."
Obama's health care law requires most insurance plans to cover women's preventative services, without a co-pay, starting on Aug. 1, 2012. Those services include well women visits, domestic violence screening and contraception, all designed to encourage health care that many women may otherwise find unaffordable.
The Associated Press contributed to this report.