The shelter's manager said that at least a dozen intoxicated men had attacked staffers Saturday night and police arrested two after witnessing them strike employees.
"Anyone that physically assaults a client or staff member is permanently barred from our shelter," said shelter manager Linda Trotter. "They are able to access other shelters in the city."
But several men said they were forbidden from entering the shelter, in the 600 block of Fallsway, even though they had no role in the altercation. They said they did not know why or for how long they were banned, or how they could protest the decision.
"There's a lot of confusion," said Michelle Ewert, a staff attorney with the Homeless Persons Representation Project. "People who stay in the shelter aren't given a lot of information."
The city's directors of human services and homeless services did not respond Monday to requests for comments.
A spokesman for Mayor Stephanie Rawlings-Blake said Monday evening that the city would not tolerate violence at the shelter. He referred questions to police.
"It's a police incident," said spokesman Ryan O'Doherty. "There was a fight between clients. A staff member was attacked."
Police representatives said they were unable to immediately produce the police report.
Five homeless men who spoke with The Baltimore Sun offered a different account of events. They said that after two men got into a fight, staffers beat a third man, Thomas Nowlin, 31.
"They attacked me," said Nowlin, who said he was trying to break up the fight.
Nowlin was charged with assault. He filed a counterclaim against shelter staffers, charging them with assault.
Ronald Williams, 27, said that he had been involved in the fight, but that Nowlin was an innocent bystander.
"The staff attacked him to try to shut him up," Williams said.
Ewert said the advocacy group was concerned about the allegations of retaliation, and wanted to know if some of the men were banned for recounting their version of events to police.
"Our concern is that people are being dissuaded from speaking with law enforcement," she said.
City officials had previously assured homeless advocates that they could create and adhere to a set process for banning people from the facility, Ewert said.
Williams said staff members were correct to expel him from the premises, but that other homeless men there had been wrongfully forced from the facility, including Joey Wooters, 27, whose only crime he says was being friends with Williams.
Jason Walker, 27, said that he was barred from the shelter even though he was not involved in the fight. He said he did not know why or for how long he had been banned.
Williams and Wooters said they were speaking out about their treatment at the shelter to prove to City Hall that homeless people can make their voices heard.
"They think no one's going to listen to us, because we're homeless," Williams said. "We're trying to do the right thing. We're barely surviving as it is."
Baltimore Sun reporter Scott Calvert contributed to this article.