BERNARDS TOWNSHIP, N.J. — Mohammad Ali Chaudry, a retired financial officer, has lived in this prosperous town for 40 years. It is where he raised his three children and where he served as mayor, and before that, as a member of the school board. It was also where Mr. Chaudry, an observant Muslim, always wanted to pray.
But Mr. Chaudry and some 70 fellow Muslims have been stymied for years in their quest to build a mosque on a four-acre plot of land in Basking Ridge, a genteel community here that is as proud of its old oak trees as its old homes. A year ago, after 39 public hearings in which local officials and residents picked apart every aspect of the proposed mosque, the planning board rejected the proposal, citing issues like storm water management and pedestrian safety in the parking lot.
Now, the federal Justice Department has filed a lawsuit against Bernards Township, arguing that its decision violated federal law and discriminated against the applicants purely because of their Muslim faith. The complaint, filed last month, follows a lawsuit brought by Mr. Chaudry’s Islamic Society of Basking Ridge, which has been subjected to anti-Muslim fliers and social media posts and even vandalism.
During the protracted application process, someone stomped on the group’s mailbox and later superimposed “ISIS” over the society’s initials on the mailbox. “This was unprecedented,” said Mr. Chaudry, the society’s president, who holds a Ph.D. in economics from Tufts University and teaches a course at Rutgers University on Islam. “No other house of worship in the township’s history had ever been treated the way we were.”
Across the country, more and more towns have used local zoning laws as barriers to new mosques and Islamic schools, underscoring what civil rights advocates say is a growing wave of intolerance that has been amplified by the victory of President-elect Donald J. Trump. In response, the federal government has been increasingly turning to the courts, using a law passed unanimously by Congress in 2000 that prohibits municipalities from discriminating against religions in land-use decisions or treating religious groups differently than secular ones.
While the law, with the arcane name Religious Land Use and Institutionalized Persons Act, was intended to protect all religious faiths, 11 of the last 13 cases brought by the Justice Department — including three in the last month — have involved Muslims.
“The law, by its very nature, deals with particularly vulnerable populations,” said Mark Goldfeder, a senior lecturer at Emory University’s School of Law and a senior fellow at the university’s Center for the Study of Law and Religion. “It’s so easy for towns to hide discrimination behind layers of land-use procedure.”
But Muslim advocates and experts on religious freedom worry that Mr. Trump’s impending inauguration leaves the future of the powerful religious freedom law in doubt. The man the president-elect has nominated to lead the Justice Department, Senator Jeff Sessions, Republican of Alabama, has endorsed Mr. Trump’s call for a temporary ban on immigration from Muslim countries.
As the nation’s chief law enforcement officer, Mr. Sessions might be less sympathetic to pursuing investigations involving the rights of Muslims. There are now 13 open land-use investigations under the law, though a spokesman for the department declined to say how many of those involved mosques.
Ross K. Baker, a distinguished professor of political science at Rutgers who has studied the federal law, said it was “entirely possible” Mr. Sessions could choose to dial back on the investigations. “It is within the province of the attorney general-designate to decide whether to proceed with a lawsuit,” he said.
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