A federal judge did not dismiss a lawsuit challenging the University of Notre Dame's private agreement with federal agencies that exempts it from providing contraceptive care to those on its health care plan.

The case was brought by Irish 4 Reproductive Health, Natasha Reifenberg and Jane Does 1-3 against the university and the Department of Health and Human Services, Department of Labor and Department of Treasury.

The lawsuit concerns a private settlement agreement between the federal agencies and Notre Dame that exempts the university from existing and future requirements for contraceptive coverage.

In the lawsuit, the plaintiffs allege the government's Interim Final Rules, that allow an exemption based on religious objections, violates the procedural requirements of the Administrative Procedures Act because there was no public notice or comment before the rules went into effect.

The plaintiffs also allege the settlement agreement is illegal and unconstitutional because it was made privately without input from university students and staff and essentially promotes one religion over another. They also allege it is contrary to the Women's Health Amendment of the Affordable Care Act.

In his January 16 decision, federal Judge Philip Simon granted dismissal on two of the constitutional challenges, but did not grant dismissal on five of the counts in the amended complaint.

Judge Simon found in favor of the plaintiff that the settlement agreement and Interim Final Rules are subject to judicial review and the plaintiffs have standing in the case.

He also found the rules and settlement agreement could be seen as promoting one religion over another, which could violate the Establishment Clause.

"I think the allegations are sufficient at this juncture to allege that the Rules and Settlement Agreement both impermissibly advance religion. If, in purporting to accommodate the religious exercise of some, the government imposes costs and burdens of that religious exercise on others, it favors the faith of the benefitted over the benefits and rights of the burdened, and this could violate the Establishment Clause."

The judge granted dismissal on the allegations the rules and agreement violate the Due Process Clause and Equal Protection Clause.

"The motions will largely be denied because Plaintiffs have stated plausible claims that the Final Rules violate the procedural requirements of the APA, the Settlement Agreement and Final Rules substantively violate the APA, the Settlement Agreement is void for illegality, and the Settlement Agreement and Rules violate the Establishment Clause. Dismissal is only warranted for two of the constitutional claims."