The Center of Supervision on Mosques Affairs - The Justice Department's probe comes a week after the Islamic Society of Basking Ridge sued Bernards Township in federal court, alleging religious infringement.
The lawsuit alleges a very lengthy process during which the town’s planning board made references to terrorism and questioned what children would learn in the mosque.
The planning board also expressed concerns about storm water drainage and a buffer zone between the proposed mosque and a neighboring property.
"What should have been a simple board approval for a permitted use devolved into a Kafkaesque process that spanned an unprecedented four years and included 39 public hearings," the suit said.
The attorney representing the Islamic Society of Basking Ridge, Adeel Mangi, declined comment on the federal investigation.
The group's founder, Mohmmad Chaundry, is a longtime city resident who once served on the town's school board.
The group is suing under the Religious Land Use and Institutionalized Persons Act, which gives religious institutions a way to avoid burdensome zoning law restrictions on their property use.
The 2000 federal law also prohibits the imposition of burdens on the ability of prisoners to worship as they please.
The Justice Department 's Civil Rights Division is tasked with enforcing federal statutes prohibiting discrimination on the basis of race, color, sex, disability, religion, familial status and national origin.
Bernards Township Mayor Carol Bianchi told The Associated Press that town officials will cooperate with federal authorities.