Atlanta police officers and agents from the Georgia Bureau of Investigation swarmed a house this week that has long been known in the city as a hub of activism.

Three people were arrested inside, charged with money laundering and charity fraud for spending connected to the Atlanta Solidarity Fund, which has paid bail and provided legal support for protesters fighting plans for a new police and fire training complex widely known by its derisive nickname, “Cop City.”

Civil liberties groups and a number of elected officials have condemned the charges as egregious retaliation for lawful protests. The arrests have inflamed an already tense situation: For months, law enforcement officials have been cracking down on protests against the training center.

Kamau Franklin, a community organizer in Atlanta, said on Friday that opponents of the center saw the latest arrests as part of a larger bid to chill protests and scare would-be activists out of being involved in social justice movements. “We’re in dangerous times,” he said. “Law enforcement is now attacking the very infrastructure of organization and movement politics.”

But officials contended that the arrests reflected something far more sinister: “These criminals facilitated and encouraged domestic terrorism,” said Georgia’s governor, Brian Kemp.

The charges should be seen as a potent reminder that “we will track down every member of a criminal organization, from violent foot soldiers to their uncaring leaders,” Mr. Kemp said in a statement on Wednesday. “We will not rest until they are arrested, tried and face punishment.”

The conflicting reactions to the charges are an extension of a broader disconnect in Atlanta between opponents and supporters of the planned police complex, as an effort to stop the construction of the training center amid a 1,000-acre stretch of urban forest land escalated into violent clashes in the woods, leading to the fatal shooting of one activist and domestic terrorism charges against many protesters.

The three people arrested — Marlon Kautz, 39; Savannah Patterson, 30; and Adele MacLean, 42 — made an initial court appearance on Friday. Bail for each of them was set at $15,000. But Judge James Altman expressed some skepticism about the state’s case. “I don’t find it real impressive,” he told prosecutors during the hearing, adding that “there’s not a lot of meat on the bones of thousands of dollars going to illegal activities.”

The three have been accused, according to arrest warrants, of misleading donors by spending money to support Defend the Atlanta Forest, a group that has been blamed by local authorities for the arson and vandalism of buildings and heavy equipment during protests, and for throwing Molotov cocktails, rocks and fireworks at uniformed police officers.

The warrants listed specific reimbursements to the three from Mr. Kautz’s charity, registered as the Network for Strong Communities, which runs the Atlanta Solidarity Fund: $298.54 to Mr. Kautz for mesh communications equipment to monitor the forest, $115.80 to Ms. Patterson for camping supplies, and $29.72 to Ms. McLean for a safe bought from Amazon, among other expenses.

The authorities also noted that $48,000 had been transferred by the Network for Strong Communities to another organization, which then returned the money — actions that prosecutors said constituted money laundering.

During the hearing, prosecutors said that the defendants’ work might appear lawful, even laudable, but that their money had helped fund destructive acts, including violent protests related to the training facility and vandalizing Ebenezer Baptist Church, the storied Atlanta congregation led by the Rev. Dr. Martin Luther King Jr. and Senator Raphael Warnock.

John Fowler, a deputy attorney general, also said that they “harbor extremist anti-government and anti-establishment views.” (The case is being prosecuted by the Georgia attorney general’s office and the district attorney for DeKalb County.)

But Donald Samuel, a lawyer for the three defendants, said they had done nothing wrong. “The notion that the solidarity fund should be somehow responsible for everything that goes over the line seems unbelievably unjust to me,” he said on Friday.

The Atlanta Solidarity Fund, the group that the three are associated with, said it saw the charges as an effort to hamper protesters’ ability to access legal aid.

Legal experts said that prosecutors could face significant hurdles as the case moved forward. Charitable organizations have First Amendment rights, and they routinely reimburse people for expenses like the ones cited in the arrest affidavits. The Network for Strong Communities lists the bail fund, pursuing police accountability and training community activists among its initiatives. To prove fraud, prosecutors would have to show that donations were used for other purposes.

“It’s a stretch to use what are white-collar financial fraud claims to charge these individuals, but obviously they want them charged,” said Randy Chartash, a former federal prosecutor of white-collar crime who is now a criminal defense lawyer in Atlanta. Still, he said, it is common for prosecutors to bring unrelated charges such as tax evasion against someone they believe to be involved in crime.

Money laundering in this context would typically refer to an attempt to conceal the source of funds or the use of funds to promote criminal activity, Mr. Chartash said, adding, “This will be a difficult case to prove.”

But the arrests have also stoked concerns that reach beyond the case itself. Josh McLaurin, a Democratic state senator representing an Atlanta suburb, called the raid “reckless,” saying, “The situation is already at a fever pitch.”

The fight over the stretch of woodland, an old prison farm that had been reclaimed by nature, has gone on for nearly two years.

Plans for the roughly $90 million facility include areas for police trainees to learn vehicle skills, as well as a nightclub, a convenient store and homes, all intended to better prepare officers but also lift a police force that has been depleted of morale and manpower in recent years.

The development has been challenged not just by activists opposed to the aggressive police tactics and increased militarization of police forces that they argue the facility will support, but also by environmental advocates who want to protect a rare remaining expanse of green space near Atlanta.

Tensions came to a head during a violent confrontation between protesters and law enforcement officers in January, when a 26-year-old environmental activist named Manuel Esteban Paez Terán was fatally shot and a state trooper was wounded.

Some of those concerned about the crackdown on protesters say that the debate over the training center has particular resonance in Atlanta because of the city’s deep ties to the civil rights movement and the role of protests in shaping the city’s identity.

“Because of our reputation, Atlanta has to set the bar in terms of what freedom of speech looks like,” said Liliana Bakhtiari, a city councilor representing the area in East Atlanta where the three were arrested, and a critic of the planned facility. “The state’s actions against us, and what they are conducting in our city, I find to be a direct threat to that legacy and to the spirit of what Atlanta is.”

Chris Carr, the state attorney general, said Georgia would press forward in prosecuting cases related to the protests. “We will not rest,” he said in a statement, “until we have held accountable every person who has funded, organized or participated in this violence and intimidation.”

But Ruwa Romman, a Democratic state representative from Duluth, northeast of Atlanta, expressed a sense of exhaustion — not just with the aggressive response to protesters, but also with the push to continue constructing the facility.

She said the project should have been paused after the shooting death of the activist, known as Tortuguita. “But,” she said, “the only message that I’m seeing being told to law enforcement is that, ‘No matter what you do, we will make sure you get whatever you need, at all costs.’”

Shaila Dewan contributed reporting.