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Pro-life Democrats Ben Nelson of Nebraska, Robert P. Casey Jr. of Pennsylvania and Joe Manchin III of West Virginia voted for the amendment, but some moderate Republicans expressed concern over the legislation’s sweeping language. Retiring Sen. Olympia J. Snowe of Maine voted against it, while her colleague Susan M. Collins supported it despite strong reservations.

Ms. Collins said she wrote a letter to the administration asking for clarification on whether religious employers who self-insure also would be exempt from the mandate — but the administration was vague in its response. The administration also has formally written the initial regulation into law but has not done the same for its proposed fixes.

“I do this with a lot of conflict, because I think the amendment does have its flaws,” she said. “But when the administration cannot even assure me that self-insured organizations’ religious freedoms are protected, I feel I have no choice.”

As the most vocal opponent against the contraception mandate, the U.S. Conference of Catholic Bishops vowed to continue opposing the rule and said it is looking to similar legislation that House Republicans have indicated they will advance.

“We will continue our strong defense of conscience rights through all available legal means,” said Bishop William E. Lori of Bridgeport, Conn. “Religious freedom is at the heart of democracy and rooted in the dignity of every human person. We will not rest until the protection of conscience rights is restored and the First Amendment is returned to its place of respect in the Bill of Rights.”

House Speaker John A. Boehner, Ohio Republican, promised eventual action on similar legislation, but didn’t set a timetable Thursday.

That left the issue to roil the political field, with parties and pressure groups on both sides of the aisle vowing to keep the issue at the forefront of public discussion until November.

“We know this is just an attempt in a series of attempts,” said Sen. Patty Murray, Washington Democrat. “We heard from Sen. Blunt today that they’re going to continue to move forward, to go after taking away the ability of women to make their own health care choices, particularly when it comes to contraceptives. We’re going to stand up, we’re going to fight back.”

Terry O’Neill, president of the National Organization for Women, vowed that “without question, the politicians who voted in favor of Blunt’s amendment — whether female or male, Republican or Democrat — will pay a price in the voting booth.”

The Republican presidential candidates have seized on the issue to cast doubt on Mr. Obama’s commitment to religious liberty. In a CNN presidential debate last month, former Massachusetts Gov. Mitt Romney said the mandate was a continuation of the president’s attack on religion.

“I don’t think we’ve seen in the history of this country the kind of attack on religious conscience, religious freedom, religious tolerance than we’ve seen under Barack Obama,” Mr. Romney said.

Marjorie Dannenfelser, president of the Susan B. Anthony List, which supports pro-life candidates, said, “There will be consequences in November for senators in tight races who voted to kill this amendment with the absurd reasoning that they are acting in the best interests of women. Undermining the religious liberty and conscience rights of women can never serve them.”

• Cheryl Wetzstein contributed to this report.