By Tierney Sneed and Tami Luhby, CNN

(CNN) — A judge paused in two Southern states a new federal mandate that employers give workers seeking elective abortions time off to obtain and recover from the procedure.

US District Judge David C. Joseph in a Monday order partially halted the new rule being implemented by the Equal Employment Opportunity Commission, saying the agency had exceeded the authority given to it by Congress in putting forward the regulation. The rule is set to take effect Tuesday, but Joseph has blocked the agency from enforcing it in Louisiana and Mississippi, while the states’ legal challenge to the regulation plays out. Joseph’s order also halts the enforcement of the rule against four Catholic entities that brought their own lawsuit.

In April, the EEOC released the final rule under the Pregnant Workers Fairness Act, which Congress passed as part of a broader federal spending package in 2022. The act, which became law a year ago, requires that workplaces make certain accommodations for pregnant employees “related to the pregnancy, childbirth, or related medical conditions” and applies to employers with at least 15 workers unless the accommodations would cause “undue hardship” for the employer.

The final regulation clarified the provisions of the act, including the controversial measure to include abortion in the act’s definition of “pregnancy, childbirth, or related medical conditions” – which sparked a flurry of comments to the commission, with about 54,000 of them urging the agency to exclude abortion and about 40,000 comments asking to include it.

“If Congress had intended to mandate that employers accommodate elective abortions under the PWFA, it would have spoken clearly when enacting the statute, particularly given the enormous social, religious, and political importance of the abortion issue in our nation at this time (and, indeed, over the past 50 years),” Joseph, an appointee of former President Donald Trump, said in his opinion.

The judge said his preliminary injunction did not apply to “terminations of pregnancy or abortions stemming from the underlying treatment of a medical condition related to pregnancy.”

When it issued the final rule, the EEOC noted that the law cannot be used to require a job-based health plan to pay for any procedure, including an abortion. It specified that the act is a workplace anti-discrimination law.

The act provides pregnant and postpartum workers with a variety of protections, including time off for recovery from childbirth, prenatal or postnatal appointments and postpartum depression and accommodations related to seating, light duty, breaks for food, water and restroom needs, breastfeeding and miscarriage. Employers are not required to offer paid time off.

“In its ruling, the court disregarded decades of legal precedent. ‘Related medical conditions’ to pregnancy have long been interpreted to include abortion,” Dina Bakst, co-president of A Better Balance, a national legal advocacy organization, said in a statement. “It is important for pregnant and postpartum workers to understand that this ruling does not mean their rights under the Pregnant Workers Fairness Act have been taken away, and that the ruling does not affect the rest of the regulations.”

Monday’s order comes on the heels of a Friday ruling by an Arkansas federal judge that dismissed a challenge to the new abortion rule brought by Arkansas and 16 other states. The judge in that case, Obama-appointed US District Judge D.P. Marshall Jr., cited last week’s Supreme Court opinion in a major challenge to abortion pill access and said that the states lacked standing to bring the lawsuit.

This story has been updated with additional information.

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