Last month, the Obama administration issued new regulations concerning the so-called “conscience clause,” which permitted health-care workers to refuse to perform services that they felt conflicted with their deeply held religious or moral beliefs. This replaces a Bush-era regulation that was designed to protect health-care workers from acting contrary to their consciences or religious beliefs.

The central core of the original clause, which protects doctors and nurses from performing abortions or sterilizations to which they have a religious objection, remains. The balance of the regulation, which had extended conscience protections to others, such as pharmacists or other health-care workers, has essentially disappeared.

The earlier regulation, which was enacted at the end of the Bush administration, cut off federal funding for thousands of health-care institutions such as hospitals and clinics, both religiously affiliated and government-run, if they did not accommodate employees who refuse to participate in health-care decisions or procedures that they feel violate their personal, moral or religious beliefs.

While not perfect, this regulation was designed to prevent outright discrimination against religious employees, while still permitting those entities to accommodate and retain those employees. The regulation also prevented discrimination by religious institutions against health-care providers such as doctors who, in the exercise of their own consciences, would perform such procedures — say, in their personal practice away from the religious institution itself.

The Obama administration reverses that commonsense accommodation. First, it skirts the language of the federal conscience statute, which is not limited to abortion or sterilization, as the Obama administration regulation is. The regulation instead will allow discrimination against religious employees, and not to accommodate them. Moreover, the decision eliminates some crucial definitions that protected religious employees. The administration explained that “individual investigations will provide the best means of answering questions about the application of the statutes in particular circumstances.” This should not provide comfort to religious believers.

The decision also demonstrates the transformation of the debates over conscience and religious liberty, one not generally noticed. Traditionally, discussions about religious liberty involve two parties: the individuals and the state. The Constitution was designed to protect individuals against the power of the state to act contrary to their beliefs.

Now, the debate over religious liberty has changed; it more often revolves around the state being an active participant in a market (such as health care) and using its power to take one side or another in a debate between essentially private parties. This change has been disguised because the government’s action is usually couched in “rights” language, such as supporting “consumer choice” or “autonomy.” Thus, states have forced pharmacists to provide Plan B or other medications contrary to their religious beliefs, in the name of access or consumer choice. The desires of individuals to have certain services performed or options available must, on this view, trump the religious liberty of people who wish to refuse providing those services or options.

As Robert Vischer, a law professor whose recent book Conscience and Common Good traces these developments, states, “the fact that the state cannot forbid the provision of a particular good or service is taken to mean that every good or service must be provided by all licensed providers. In the process, the moral convictions of providers are rendered irrelevant.” Religious people should be very sensitive to this change in emphasis.

In the future, Catholic or other religious institutions will face more circumstances in which the state sides against the religious person or institution. This stance presents a danger to both the constitutional protections of religious freedom, as well as a threat to the diversity of moral viewpoints represented in the public square by religiously affiliated institutions.

Religious institutions should undertake some soul-searching of their own. By their nature, these regulations apply only to those institutions that receive federal funding. Because so many health-care institutions are run by religious entities, and receive federal funding, they are always at the mercy of changing political winds. In light of the restricting of the rights of conscience, and the changing assumptions underlying how the political discourse treats political liberty, such institutions need to reconsider their relationship with the state and government funding.

In a related, ominous note, The Washington Post has reported that the federal Centers for Medicare and Medicaid Services is investigating a complaint that religiously affiliated hospitals are violating federal law by refusing to provide certain types of care on religious grounds. That is, these institutions are expressing their religious identity, something that can run them afoul of regulations such as these.

Indeed, opposition to Catholic or other religious hospitals from expanding and providing more care is growing, for fear that those hospitals will actually practice according to their religious beliefs.

In a time of looming government bankruptcy and the increasing health-care needs of the poor, ideology should not be permitted to trump religious liberty.

Gerald J. Russello is a fellow of the Chesterton Institute at Seton Hall University.