They allege that giving money to the two institutions violates the state constitution, which prohibits tax dollars going to ministries or places of worship. ACLU officials said the state had blurred what should be a clear line of separation between church and state.
"Our position is that while New Jersey should support our colleges and universities, it cannot do so at the expense of the separation of church and state," said Udi Ofer, the state ACLU's executive director.
The ACLU has asked for a preliminary injunction to immediately prevent the state from dispensing money to the two institutions. Ofer said the goal was to halt the funding before construction begins. A hearing is set for 9 a.m. Friday in Superior Court in Trenton.
The $1.3 billion comes from five sources, the bulk from the Building Our Future Bond Act, approved by voters in a November referendum.
In April, the state secretary of higher education announced the 46 grantees. Beth Medrash Govoha was awarded $10.6 million for a library, research center, and academic space. Princeton Theological Seminary was to receive $645,323.
The Legislature had 60 days from the date the projects were announced to approve or reject all 46 as a group. The deadline for that action is Friday.
While the plaintiffs said they were against public funds going to the two institutions they have targeted, they said they did not oppose tax dollars going to the 44 remaining schools, which are secular.
They said the suit aims at the separation of church and state and not the right to teach religion.
"We support religious training, but it can't be done with public funds," said the Rev. Craig Hirshberg, executive director of the Unitarian group.
Anderson said she supported the grants in the referendum but was "outraged" to learn that two religiously affiliated schools were grantees.
Assembly Speaker Sheila Oliver (D., Essex) did not immediately respond to a request for comment Monday.
Last month, in an Assembly resolution to reject the $1.3 billion aid package for the schools, she wrote, "These grants may be subject to challenge under the establishment clause of the U.S. Constitution as a violation of the separation of church and state."
Gov. Christie accused Oliver of playing politics and said Beth Medrash Govoha had received $46 million from the Tuition Aid Grant Program since 2000, which Oliver had never challenged.
The governor's office did not respond to calls for comment Monday.
The ACLU also says giving money to Beth Medrash Govoha violates New Jersey law because the yeshiva has only male students.
A spokeswoman for the Princeton Theological Seminary said the school had no comment on the litigation.
Responding to a request for comment, Beth Medrash Govoha vice president for administration Moshe Gleiberman wrote in an e-mail that the school's "educational programs focus on studies such as Talmud and Hebrew language and literature," and the requested funds would be used "solely to expand library facilities and academic capacity."
Contact Sean Carlin at 856-779-3237, firstname.lastname@example.org, or follow on Twitter @SeanCarlin84.