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.

Image A rendering of the proposed mosque. Credit... Karsten Moran for The New York Times

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.

Another recent case brought by the department involved a proposed mosque in Virginia. The lawsuit argued that Culpeper County violated the religious land-use law in denying a sewage permit application. The complaint noted that since 1992, the county had considered 26 applications and never before denied such a permit to either a commercial or religious group.

In a speech this month at a Virginia mosque, Loretta E. Lynch, United States the attorney general, talked about the department’s response to a surge in hate crimes, highlighting enforcement of the land-use law. “Members of the Civil Rights Division have heard repeatedly about more overt discrimination in both the tone and framing of objections to planned religious institutions, especially mosques and Islamic centers,” said Ms. Lynch, who sent a letter to state and local officials on Thursday reminding them of the law and their obligation to respect religious freedom.

In the case of Bernards Township, the Islamic Society bought land that was in a zone that permitted a house of worship. Raising money from various sources, Mr. Chaudry oversaw the purchase of four acres, aware that the zoning code required at least three acres for a house of worship.

The society hired an architect who took pains to design a mosque that would blend in with the neighborhood, where a fire station stands across the street from the site. The 4,400-square-foot mosque, the size of a large house, would forgo the traditional dome and would include minarets that mimic the chimneys on neighboring houses.

“The mosque proposal met with vociferous public opposition,” the Justice Department wrote in its recent complaint. “Fliers, social media and websites denounced the mosque and were filled with anti-Muslim bigotry and references to terrorism and the 9/11 attacks.”