Several religious groups are dismayed and confused by the Trump administration's move, including the Little Sisters of the Poor a group of nuns that fought the mandate for several years but expected an immediate reprieve under the GOP president. They believed either the Justice Department would halt its appeal in the case or the administration would seek a rules change from the Department of Health and Human Services.
Trump promised during the campaign that he'd side with the mandate's opponents, indicating to Catholic leaders that as president he would ensure the requirement was lifted.
"I will make absolutely certain religious orders like The Little Sisters of the Poor are not bullied by the federal government because of their religious beliefs," Trump wrote in a letter to the Catholic Leadership Conference.
The fight over whether employers with religious objections to birth control should have to pay for it emerged as one of several high-profile battles involving President Barack Obama's sweeping 2010 health-care law. The law requires employer-sponsored health coverage to include certain preventive services the Obama administration interpreted that to include all FDA-approved contraception.
The Obama administration gave religious colleges, schools and charities a way out from providing contraception coverage by allowing them to delegate that job to a third party. Under a Supreme Court ruling, certain corporations can now take that route, too.
But some religious nonprofits still say that doesn't go far enough, and instead want to be fully exempted from the mandate in the same way as churches. In May, the Supreme Court tossed those cases back to appeals courts, directing them to guide the Obama administration and the nonprofits toward working out a compromise.
East Texas Baptist University and other plaintiffs represented by the nonprofit law firm Becket are now asking the Justice Department to drop its appeal of a district-court ruling in their favor, allowing them permanent relief from the mandate.
"This litigation has gone on long enough," the plaintiffs wrote in a petition last week to the Fifth Circuit. "It is time for the Department of Justice to move on, and to allow the court, the universities and other religious ministries to move on as well."
But Justice argued in its petition to the Fifth Circuit that it needs more time to litigate the case because numerous Cabinet and subcabinet positions in several federal agencies involved remain unfilled several months into the new administration.
"The issues presented by the Supreme Court's remand order are complex," the Justice Department wrote.
Conservatives who oppose the birth control mandate on religious liberty grounds are bewildered by the move at a Justice Department headed by former Sen. Jeff Sessions, R-Ala., who is well known for his conservative views.
And many had expected the Department of Health and Human Services, now led by another conservative, former representative Tom Price, R-Ga., to change the Obama administration's underlying rule to fully exempt religious colleges, schools and charities from covering birth control. But HHS has not proposed any rule changes and didn't respond to a request Monday about whether there are plans to do so.
As things stand now, it appears that Justice plans to continue defending the way the Obama administration applied the birth-control mandate, said Eric Rassbach, a Becket attorney.
"That just seems to be very contrary to what they've been saying publicly," Rassbach said.