The Bush administration had signaled its intention to issue the measures, which are part of a flurry of regulations it is announcing before President-elect Barack Obama takes office. The new president will be able to undo the regulations, and is virtually certain to, given his previous comments on the issue. But undoing them will be a time-consuming process.

The measures announced on Thursday, sometimes described collectively as the “conscience rule,” were issued just in time to take effect before the start of the new administration. They will go into effect 30 days after their publication in the Federal Register on Friday. Recipients of funds from the Department of Health and Human Services are required to certify their compliance with the rule by October 2009.

“If, despite the department’s efforts, compliance is not achieved, H.H.S. officials will consider all legal options, including termination of funding and the return of funds paid out in violation of the non-discrimination provisions,” Mr. Leavitt said.

Opponents of abortion, including the United States Conference of Catholic Bishops and the Catholic Health Association, which represents Catholic hospitals, support the new regulations and say they are needed to protect health-care providers from being forced to perform abortions and sterilizations.

They are opposed by the National Association of Chain Drug Stores, the American Hospital Association and the American Medical Association, among others. Opponents contend that the regulations are a threat to a woman’s right to choose to have an abortion, and that they are not needed in any event because the Civil Rights Act of 1964 already prohibits employment discrimination based on religion.