The officers who arrested Brenda Wernikoff are now being investigated by the department’s internal affairs division.

The department is also continuing to work on training its officers on how to interact with the transgender community.

According to Wernikoff, Boston police did not just book her, they humiliated her.

After she was arrested for refusing to leave a woman’s bathroom at a homeless shelter, she said four to five male officers at the South End police station forced her to remove her shirt and bra and expose her breasts.

According to the federal lawsuit, “The officers then ordered Ms. Wernikoff to jump and down, causing her breasts to jiggle” as the officers laughed. “I mean belly laughs,” Wernikoff said, describing the May 2010 incident.

“The officers contend that was pure fiction. They are well-respected veterans of the department,” said Kenneth Anderson, a lawyer who is representing the officers in the department’s investigation.

Cheryl Fiandaca, spokeswoman for the Boston police, declined to comment on the lawsuit, but she said top commanders have been meeting with leaders in the transgender community about such issues.

“Currently, we are working with the Massachusetts Transgender Political Coalition to develop new policies to deal with various situations and issues of importance that could arise with the police and the community,” she said.

Last Friday, the Boston Public Health Commission, which runs the Woods Mullen Shelter where Wernikoff was arrested, agreed to pay her an additional $10,000. Staff members at the shelter, who called police that day, were retrained after the incident, said commission spokesman Nick Martin.

“We place an extremely high priority on having policies that promote inclusivity and prohibit discrimination,” he said. “The commission has a clear policy to support transgender individuals — a policy that was in place well before this incident and reinforced in the wake of this unfortunate experience for one of our clients.”

Wernikoff, 60, said she hopes police officers will soon have clear guidelines on how to treat transgender people.

“It shouldn’t happen again to anyone,” she said.

The City of Boston has long had an ordinance that says people have the right to use restrooms, showers, and dressing rooms based on their gender identity, a rule that goes beyond state protections of transgender people.

The problem is that the city has failed to train many officers on its own ordinance, said Wernikoff’s lawyer, Howard Friedman, a well-known civil rights attorney.

He pointed to departments in Washington, D.C., and Los Angeles, which make clear in their rules and regulations that officers are to address a transgender person by their preferred name and use appropriate personal pronouns. They also instruct officers to conduct searches in the same way that they would on a non-transgender person.

Boston police did not follow those guidelines when they arrested Wernikoff, according to the lawsuit filed last November.

Wernikoff, whose birth name is Bruce Wernikoff and who began identifying as a woman when she was in her mid-50s, had been staying at the shelter for about a year. She said she had nowhere else to go after she left her uncle’s home, where she felt unwelcome by relatives uncomfortable with her gender identity.

Wernikoff was in a bathroom stall when a counselor, Margaretta Collins, came into the bathroom and told her she could not be there when other women were present.

Collins said in an interview that her supervisor told her that transgender people at the shelter were supposed to use another bathroom on the floor.

“For whatever reason, she chose to use the female’s bathroom and the females complained,” said Collins, who left her job about a month ago for health reasons.

The Boston Public Health Commission’s policy stipulates that transgender women may use the women’s restroom and showers. Martin said staff members are instructed to follow the commission’s protocol.

“If [Collins] was unfortunately given that advice by her supervisor that would have been a mistake,” he said.