Leaders of the yellow church that has been at the center of the District’s Black Lives Matter demonstrations say they are concerned about how police cleared protesters from the area earlier this week — and upset that the city built a fence around their property in the name of safety.

Police and city workers on Monday and Tuesday cleared out people, signs, bicycles and tents — including a volunteer medical tent — from the intersection of 16th and H streets NW, in front of St. John’s Episcopal Church and across Lafayette Square from the White House.

Up went high fencing, blocking the park all along the south side of H Street, and blocking St. John’s — but not other nearby buildings — on the north side.

Episcopal Bishop Mariann Budde and the Rev. Robert Fisher, the church rector, say church leaders gave the city permission to put up fencing but believed the entire block was being cordoned off and didn’t want to be the only structure outside the barrier. Budde and Fisher also said they were caught off guard by police involvement in clearing the street.

The moves were “a surprise to us,” said Fisher, adding that church officials are trying to find a way to lower tensions on the street and once again allow protesters to access the front of the church.

“St John’s isn’t just a building. It is a community of people striving to live their faith,” Fisher said. “Our aim is to be agents of grace. And we are actively seeking how to best do that as the situation is evolving continually right around us.”

Susana Castillo, a spokeswoman for D.C. Mayor Muriel E. Bowser (D), declined to say Thursday what the city had told church officials. “We will continue to monitor the situation to ensure public health and safety are maintained,” Castillo said in a text message.

Bowser told reporters that H Street NW is being reopened to vehicles and needed cleaning to remove items causing a health or safety hazard. She also said city officials perceived new threats and tensions during protests this week.

City officials said the demonstrations had become increasingly violent — a man was charged with throwing a molotov cocktail at a police officer Tuesday night, and some officers were hurt. They also said a grill set up by protesters in front of the church was a fire hazard, and Bowser’s chief of staff, John Falcicchio, said people were defecating and urinating on the church.

Budde said police told her that officials were worried about the largely wooden structure catching fire, especially after the molotov cocktail incident. On May 31, as protests against police brutality led to looting and property damage, there was a small fire in the church basement that appeared to have been triggered by someone throwing an igniting substance through a window.

The next day, federal law enforcement officers used gas and horses to clear the area so President Trump could walk to the front of the church to pose for cameras, holding a Bible aloft.

The area outside St. John’s had since become not only a high-profile speaking spot for pro-Black Lives Matter activists and clergy, but also a camp for homeless people evicted from Lafayette Square, as well as the backdrop to a pop-up restaurant for protesters called Earl’s.

Now it is blocked off by fencing erected by the D.C. government on city property on the north side of H Street NW. The National Park Service erected the fencing on the south side of the street, by Lafayette Square. On Wednesday night, Budde stood outside the church, which is part of the Episcopal Diocese of Washington that she oversees, and seemed pained by what she saw.

“It looks like the only reason that the police are here right now is to guard the church, and I don’t know who ordered that because I certainly didn’t, our director didn’t,” she said.

“We obviously don’t want our church to burn down, but we also don’t want the police to be on our behalf escalating their presence and interactions.”

As police pushed down H Street on Tuesday morning — tearing down signs and clearing tents — volunteers from the D.C. Aid Station outside the church tried to tell officials they were medics and noted they had permission from St. John’s to be there.

Eric Otani, 30, who said he had been helping pull injured demonstrators out of crowds and over to medic stations almost daily since the protests began last month, paced up and down the police line, shouting.

“We were here to help people,” said Otani, as his team watched its items hauled off in city trucks.

Asked about the confrontations between police and protesters, Bowser said: “We need people to be peaceful. We need people to act lawfully. We can’t have our police officers assaulted.”

Falcicchio said the city is considering turning Black Lives Matter Plaza — the stretch of 16th Street between H and K streets NW — into a permanent pedestrians-only plaza. He said the fencing would remain up around St. John’s indefinitely.