CULPEPER, Va. — The small Muslim community here used to pray in the historic Amtrak station, where Lyndon B. Johnson kicked off a 1960 whistle-stop tour. When a local history museum moved into the space in 2014, they shifted to an empty home next to an auto business.

After years of drifting, the group of about 12 to 20 Muslims who show up regularly for Friday prayers want a more permanent place of worship. So they set out to build a mosque in a more rural area outside town.

But those plans were put on hold in April, when the county denied them a permit to haul waste from the property, which is too undeveloped for sewer service. Now the Justice Department is investigating whether that decision was based on more than the technicalities of development – and amounts to illegal religious discrimination.

“We just want our rights to be fulfilled,” said Fuad Abu-Taleb, who leads Culpeper’s Muslim prayers.

The investigation is one of 14 being conducted by the Justice Department into potential discrimination by state and local governments involving land use or jails. While the agency declined to provide details of those, more than a third of Justice Department investigations into land or institutional religious discrimination in the past six years involve Muslims – a striking statistic given that Muslims make up about 1 percent of the U.S. population.

In a similar case in July, the Justice Department filed suit against a township in Pennsylvania, alleging that it discriminated when it denied zoning approval to a group that wanted to build a mosque.

In June, Deputy Assistant Attorney General Vanita Gupta, head of the Justice Department’s Civil Rights Division, noted that the department sometimes sees “overt animus” toward religious groups seeking to build. “But we also see people organizing to try to block construction of minority places of worship often adopting more subtle tactics,” she said.

There is no question that the decision on what would normally be a little-noticed development matter in Culpeper got a lot of attention. A crowd packed the county government meeting and cheered when the motion to deny the permit was introduced. Board members reported receiving scores of calls and emails on the normally obscure land-use concern. The decision, made in a 4-to-3 vote, was celebrated on anti-Islam websites.

Ira Lupu, a professor at George Washington University Law School, said the federal investigators will conduct interviews and examine the record to look for “anything to suggest that they have granted these permits in cases where there’s no animosity towards the people applying, and maybe even a preference.”

County Administrator John Egertson said he was “very confident that when they finish their review, they will find that we are completely compliant.” The board, he said, “acted within their policy, and they acted fairly and consistently.”

The board members who opposed the Islamic Center said they did so on technical grounds. Opponents noted that although county staff recommended approval, the pump-and-haul permits are designed for situations where no other option exists.