What happens next to the pending court challenges by the nonprofits may rest with the incoming Trump administration and the U.S. Department of Justice under the leadership of U.S. Sen. Jeff Sessions, the Alabama Republican picked to lead the agency.

“We have to get to business. Obamacare has been a catastrophic event,” Trump told The New York Times on Tuesday. He urged Republicans to repeal the law and offer a replacement within weeks.

Under the Obama administration’s accommodation, an eligible organization that objects to providing contraceptive coverage for religious reasons may self-certify its objection to its health insurance issuer or third-party administrator using a form provided by the Labor department. An organization is also permitted to self-certify its objection and provide certain information to Health and Human Services without using any particular form.

The nonprofits contend that even the writing of a letter to HHS made them complicit in the provision of contraceptives, in violation of their religious beliefs.

Federal regulators solicited the public comments after the Supreme Court in May sent seven challenges back to the lower courts to see if the government and the nonprofits could reach a compromise on how to accommodate the objections.

The justices indicated in their unsigned order in Zubik v. Burwell that based on additional briefing in the case, there appeared to be an opening for compromise. In an unusual step, the high court suggested its own possible compromise.

The federal agencies in their Monday update said the high court’s plan would not work.

Related: SCOTUS birth control compromise gets mixed reaction

“The comments demonstrate that a process like the one described in the court’s supplemental briefing order would not be acceptable to those with religious objections to the contraceptive-coverage requirement,” the agencies said. “Further, a number of comments illustrate that the administrative and operational challenges to a process like the one described in the court’s order are more significant than the departments had previously understood and would potentially undermine women’s access to full and equal coverage.”

Appellate courts put on hold a series of religious-objector cases to allow the agencies and lawyers for the challengers to craft the compromise plan. The Obama administration on Tuesday began notifying the courts about the impasse and requesting the chance to continue updating the court, into the early months of the Trump administration.

“So now that this has happened, during those next status conferences, the courts will say, `How are we going to proceed?’ The real question is what will a Sessions DOJ response be,” said Brigitte Amiri, senior staff attorney at the American Civil Liberties Union’s Reproductive Freedom Project.

Amiri added: “We are waiting to see whether the act is going to be repealed in whole or in part, and we don’t know what that means for the contraception requirement.”

In its Zubik order, the Supreme Court expressed no view on the merits of the claims that the government’s accommodation burdened the exercise of religion.

The commenters included the plaintiffs in Zubik and other religiously affiliated organizations, consumer advocacy groups, women’s organizations, health insurance issuers, third-party administrators and pharmaceutical benefit managers.