Wheaton does not qualify for the administration's safe-harbor policy as a result. The college asked for an emergency injunction on Wednesday, when the new coverage policy took effect.
"In order to be eligible for the safe harbor, the institution has to certify that it has not covered contraceptives after February 10, 2012," Emily Hardman, communications director for the Becket Fund for Religious Liberty, told HuffPo.
Hardman said that Wheaton "inadvertently" covered emergency contraception "for a short time after February 10" and was still trying to fix the error at the cutoff date.
On July 18, the school filed suit over the mandate, which requires most employers to cover birth control without a co-pay in their health plans.
"Wheaton College and other distinctively Christian institutions are faced with a clear and present threat to our religious liberty" through the mandate, Wheaton President Philip Ryken said in a statement.
While Protestant teaching does not outlaw the use of birth control, as Catholic teaching does, some people in both groups consider some forms of birth control equal to abortion.
The morning-after pill is the most commonly derided form, as many believe it prevents a fertilized eggs from implanting to the uterus.
Experts recently called this understanding outdated and scientifically incorrect.
Under the White House policy, religiously affiliated institutions, such as Catholic schools, don't have to offer the coverage through their own plans. Their employees will receive free birth control directly from their insurer instead.
Churches and houses of worship are exempt from the mandate altogether.