In theory, ArchCare could have negotiated independently with the union to avoid providing its 1199 employees — health support staff members ranging from physician assistants to orderlies — abortion and contraception coverage. The archdiocese avoids providing those services for 1,100 other ArchCare employees, for example, by insuring them through a special self-insurance plan that is exempt from the mandate. But in reality, “it would be very difficult,” Mr. McIver said. “It’s hard to go backwards.”

Similar skepticism was expressed by Scott LaRue, the chief executive of ArchCare. “It doesn’t matter whether you join the league or you don’t join; the league determines the contract, and then the union goes and forces the same arrangement on the other homes whether you are in the league or not,” he said.

Religious employers nationally have often grudgingly covered contraception, whether to comply with state health care mandates or because they simply did not realize they were doing so, said Stephen S. Schneck, director of the Institute for Policy Research and Catholic Studies at the Catholic University of America, in Washington.

“It’s surprising, but a good number of employers don’t really get into the weeds that much with their insurance plans to know” if they are covering contraception and sterilization, Mr. Schneck said.

Even among the more than two dozen for-profit companies suing the Health and Human Services Department over the mandate, some were paying for contraception and other objectionable coverage until recently. They included the American Manufacturing Corporation, a mud pumping company in Minnesota whose owner, Gregory Hall, a Catholic deacon, played a pivotal role in helping to free trapped Chilean miners in 2010.

Mr. Hall’s lawyer, Tom Matthews, said his client realized that he was covering contraception for his employees only in December, when reviewing what the government would require in his next health care contract. More recently, he was “very upset” to find the plan had also been covering abortion, Mr. Matthews said. A federal court granted the company an injunction that will allow it to stop the coverage until the courts settle the matter.

Another company, Korte & Luitjohan Contractors in Illinois, found out in August that its insurance was covering abortion, contraception and sterilization “as a mistake,” according to Edward L. White, senior counsel at the American Center for Law and Justice in Washington. Korte is one of seven companies represented by the American Center in a challenge to the mandate.