WASHINGTON — The Biden administration warned the nation’s 60,000 retail pharmacies on Wednesday that they risk violating federal civil rights law if they refuse to fill prescriptions for pills that can induce abortion — the second time this week that it has used its executive authority to set up showdowns with states where abortion is now illegal.

In four pages of guidance, the federal Department of Health and Human Services ticked off a series of conditions — including miscarriage, stomach ulcers and ectopic pregnancy — that are commonly treated with drugs that can induce abortion. It warned that failing to dispense such pills “may be discriminating” on the basis of sex or disability.

The guidance came two days after Xavier Becerra, President Biden’s health secretary, instructed hospitals that even in states where abortion is now illegal, federal law requires doctors to perform abortions for pregnant women who show up in their emergency departments if they believe it is “the stabilizing treatment necessary” to resolve an emergency medical condition.

The back-to-back actions make clear that while Mr. Biden’s authority to preserve access to abortion is limited after the Supreme Court eliminated the constitutional right to the procedure last month, he will push those limits where he can. Legal experts on both sides of the issue agreed in interviews that the administration was trying to assert that federal law pre-empts that of states that have banned abortion, a move that would almost surely be challenged in court.

“They are trying to identify federal statutes that in some way will supersede state abortion restrictions and bans,” said Lawrence O. Gostin, an expert in public health law at Georgetown University. Of the guidance for pharmacists, he said, “The obvious goal is to have abortion medication in stock to treat a range of medical conditions and to be available for an abortion.”

Yet the new guidance is cautiously written, and steers clear of telling pharmacies that they have to provide the drugs for the purpose of medication abortion, which is banned or restricted in certain states. Nor does the guidance address how a provision in federal law called the Church Amendments would apply. That measure allows health care providers, including pharmacists, not to perform or assist in abortions if they have religious or moral objections.

At issue are three drugs — mifepristone, misoprostol and methotrexate — that are often prescribed for other conditions but can also induce abortions. Experts said the administration was reacting to reports that women of childbearing age are being denied the drugs after the ruling.

Mifepristone is used to manage certain patients with a hormonal disorder called Cushing’s syndrome, and misoprostol is prescribed for ulcers. But they are also authorized by the Food and Drug Administration as a two-drug combination that can be taken to terminate a pregnancy during the first 10 weeks, and can also be used in combination following miscarriages. Methotrexate is used to treat autoimmune disorders, such as rheumatoid arthritis, as well as cancer.

“These are very legitimate issues in terms of people being concerned about having access to the basic medications that they have been receiving for years, just because those medications have the capacity to end a pregnancy,” said Alina Salganicoff, the director of women’s health policy at the Kaiser Family Foundation. “It doesn’t sound like they are blocking this for men.”

The administration’s moves will almost certainly be challenged in court, and advocates for abortion rights concede that it could be a losing battle. If legal challenges work their way up to the Supreme Court, the administration will have to make its case before the same conservative supermajority who voted to overturn Roe v. Wade, the landmark legal case that established a right to abortion in 1973.

“They’re trying to mandate the stocking of abortion-inducing drugs and the performance of abortions across the nation using tools that don’t grant the federal government that authority,” said Roger Severino, who ran the Office of Civil Rights within the Department of Health and Human Services when Donald J. Trump was president. “They are trying to shoehorn abortion into laws that clearly weren’t designed to address abortion.”

Wednesday’s action could put pharmacists in a thorny position. The National Community Pharmacists Association, which represents 19,400 independent pharmacies across the country, said pharmacists “acting in good faith in accordance with their state’s laws” lacked “a clear pathway forward” and needed more guidance from states.

“States have provided very little clarity on how pharmacists should proceed in light of conflicting state and federal laws and regulations,” B. Douglas Hoey, the organization’s chief executive, said in a statement. “It is highly unfair for state and federal governments to threaten aggressive action against pharmacists who are just trying to serve their patients within new legal boundaries that are still taking shape.”

A spokesman for Walgreens, one of the nation’s largest pharmacy chains, said the company would review the guidelines; he had no further comment.

During a background call with reporters, an official from the Department of Health and Human Services said that when state and federal laws conflicted, federal law took precedent.

Mr. Biden has been under intense pressure from Democrats and advocates for reproductive rights to take bold steps to preserve the right to abortion after the court’s decision in Dobbs v. Jackson Women’s Health Organization. Among other things, they have been pushing for him to declare a public health emergency — something his administration seems unwilling to do.

Wednesday’s guidance was issued by the health department’s Office of Civil Rights. Monday’s guidance for hospitals was accompanied by a letter to health care providers, delineating their responsibilities under the Emergency Medical Treatment and Active Labor Act, known as EMTALA, a 1986 law that requires anyone coming to an emergency department to be stabilized and treated regardless of insurance status or ability to pay.

Mr. Severino argued that the guidance to hospitals “flips EMTALA on its head,” because the law defines an emergency as a condition in which the absence of immediate medical attention “could reasonably be expected to result in placing the health of the patient, or (in case of pregnancy, the unborn child) in serious jeopardy.” But Mr. Gostin took the administration’s position, saying that in the case of a pregnant woman in distress, the law permitted abortion “if it was necessary to save her life and there was no other way to stabilize her.”