The burning of a church in northern Mississippi this week is being investigated as arson because of a spray-painted message at the scene that seemed to criticize the church’s defiance of coronavirus restrictions.

First Pentecostal Church had sued the city of Holly Springs, which is about an hour southeast of Memphis, Tennessee, arguing that its stay-at-home order had violated the church’s right to free speech and interfered with its members’ ability to worship.

After firefighters put out the blaze early Wednesday, police found a message, “Bet you stay home now you hypokrits,” spray-painted on the ground near the church’s doors, according to Maj. Kelly McMillen of the Marshall County Sheriff’s Department.

A photograph of the graffiti also appears to show an atomic symbol with an “A” in the center, which is sometimes used as a logo for atheist groups.

Gov. Tate Reeves of Mississippi said on Twitter that he was “heartbroken and furious” about the fire.

McMillen said police had found a can of white spray paint and a flashlight at the scene. He said that no suspects had been identified but that investigators — including from the Bureau of Alcohol, Tobacco, Firearms and Explosives and potentially the FBI — would be going through the scene Friday.

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“We’ll probably be there till dark tomorrow night because we’re going to have to go through each and every piece of it,” he said.

After growing frustration with the city’s executive orders, the first of which was issued March 23, the church’s pastor, Jerry Waldrop, confronted city officials at a demonstration at a local Walmart. The church also filed a lawsuit against the city in April.

A lawyer for the church said in the lawsuit that police had cited Waldrop on Easter for holding a service in violation of the city’s order and had later shut down a Bible study.

In a blistering opinion filed last week in response to the lawsuit, Judge Michael Mills wrote that he feared that the church was “proceeding in an excessively reckless and cavalier manner and with insufficient respect for the enormity of the health crisis which the COVID-19 pandemic presents.”

The judge declined to block the city’s stay-at-home order, as the church had requested, and noted that the city had, in a subsequent executive order, allowed for drive-in church services.

On Friday, Nick Fish, president of American Atheists, a group that uses the logo found at the scene, strongly condemned the church burning, calling it a “heinous act of destruction.”

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“I’m disgusted that anyone would associate a symbol of our community with something so incompatible with our values as atheists,” Fish said in a statement.

Arguments over whether religious services can be held in person have become increasingly contentious in recent weeks.

Some churches in Minnesota this week said they would resume services in defiance of the governor’s orders. That followed a federal judge’s ruling in North Carolina that allowed for indoor religious gatherings after the governor said they were largely banned. In California, five lawyers with the Justice Department said in a letter to the governor that the state’s restrictions to combat the virus discriminated against religious institutions, and more than 1,200 pastors signed a declaration protesting the restrictions.

McMillen said the fire had shocked Holly Springs, a city of fewer than 8,000 people.

“Hopefully, with the Lord’s help,” he said, “we can get to the bottom of this as quickly as possible.”