When the president of the United Federation of Teachers, Randi Weingarten, opened a school in 2005 — the first ever union-run charter school in New York, and one of the only such schools in America — she promised an “oasis.” Under UFT management, she said, teachers would win a reprieve from the Bloomberg administration’s heavy-handedness, and children would benefit.

Three years later, “oasis” remains the goal, but nearly everyone involved concedes the school isn’t there yet.

With two school years completed, the total number of teachers at the school has risen to 31 from nine. Eleven teachers have left, some of them with ill will. Though many parents are happy, others have recently held an emergency meeting to criticize what they say is sometimes an unsafe environment and a dictatorial management. A tug of war is going on with the traditional public school whose building the charter school shares.

Now the school’s top administrator, Rita Danis, is announcing her resignation to parents and teachers after facing criticism from a teacher who said she was mistreated and subsequently fired in large part because she raised complaints.

“It hasn’t been the utopia that I had hoped for,” Ms. Weingarten said in an interview last week. “I think the processes that we’ve had in place are really good processes now. But we’ve had, just like every other school has, some bumps in the road.”

Problems are not unusual for a new school, especially in the tough neighborhood of East New York, where the school is housed. Yet these are particularly painful problems for a school run by the UFT, which has criticized arrangements in which charter schools share space with traditional public schools and which vowed, at the UFT Elementary Charter School, to lower teacher turnover by treating teachers fairly, to keep a safe environment for students, and to eliminate heavy-handed management.

A persistent question is how to handle the school’s unique constitution. Because Ms. Weingarten serves as both chairman of the school’s board of trustees and president of the union representing its workers, the UFT is the voice of both management and labor. To enforce the collapsed hierarchy, the person who is technically the principal is instead called the “school leader” or “teacher leader.”

The design was supposed to bring into practice in real form, at a real Brooklyn school, the union’s long-sung theory about how to improve inner-city public education — by giving teachers more freedom and “voice.”

“The UFT believes that the UFT Elementary Charter School will reveal the great bounties of educational knowledge and skill that could be tapped in all public schools, if only teachers were allowed to function as true educational professionals,” the school’s teacher handbook says.

Several teachers said the UFT’s theory is working in practice. They said they feel supported by administrators, who are constantly available to provide advice at the school’s own Teacher Center, a bright room covered in handwritten curriculum plans the teachers make together in grade-level groups. They also praised the school’s monthly “town meeting” and daily “community gathering,” where students, teachers, and administrators discuss the school’s progress.

Together, they said, staff members have been crucial in finessing the school’s unique culture — quirks such as the school’s mission code, CREST, which stands for Community, Respect, Excellence, Scholarship, and Trustworthiness, and which is now a regular part of students’ vocabulary. Yet several flare-ups have been testing the arrangement.

The most recent concluded this week, when a conflict between administrators and a teacher who had sought an outside lawyer was ended only with Ms. Weingarten’s intervention.

School officials had decided to ban the teacher, Melissa John, from returning in September after she criticized the school’s principal in a letter to state officials. Ms. John’s employment had been halted abruptly in March because of an immigration issue, but officials said they intended to take her back once the problem was worked out. Then, the teacher wrote a letter while on hiatus, and officials told her she wasn’t welcome back.

In the letter, which Ms. John provided to The New York Sun, Ms. John complained about the circumstances of her departure, saying the principal was responsible for the work permit problem that forced her to leave abruptly. She said Ms. Danis had shown “negligence, irresponsibility, untrustworthy accountability, and bias” in handling the issue. She also accused the principal of slander, saying Ms. Danis described her at a staff meeting as “untrustworthy.”

A staff member confirmed the letter’s account of the staff meeting.

Ms. Danis declined to comment on the matter.

Ms. John sent the letter to the Charter Schools Institute at the State University of New York, which oversees the UFT Elementary Charter School, and copied a UFT vice president who is on the school’s board, Michelle Bodden. Five days after the letter was sent, the UFT’s general manager, David Hickey, who also acts as the school’s business manager, told Ms. John that she would not be rehired. In an interview, Mr. Hickey said officials had been “headed” toward rehiring Ms. John — until she wrote the letter, which he called “really inappropriate.” He said the letter, combined with Ms. John’s irresponsibility in failing to resolve the immigration issue, led to the decision not to rehire. Speaking in the same interview, Ms. Bodden called Ms. John a good teacher but said: “It would be very, very difficult for her to come back with what she wrote.” Their decision was overruled last week by Ms. Weingarten, who had been on a trip to China during the incident. The reversal was part of a rethinking Ms. Weingarten described as an attempt to give the teacher “due process.” Ms. Weingarten had scheduled a meeting with Ms. John after hearing about the incident and learning the teacher was talking to a reporter.

After a second, hour-long meeting attended by Ms. John’s attorney, Roosevelt Seymour, an employment lawyer based in Brooklyn, Ms. Weingarten invited the teacher to return in September. In an interview, Ms. Weingarten said she and school officials ultimately determined that Ms. John had not been treated fairly. She said conversations began with the question of whether Ms. John is a good teacher. When everyone agreed that the answer was ‘yes,’ they collectively decided to invite her to return, Ms. Weingarten said. The union says she was retroactively placed on an unpaid leave of absence, preserving her employment.

Ms. John spoke on the record extensively before the meeting, but afterward she referred requests for comment to Mr. Seymour, who said the matter was resolved to Ms. John’s satisfaction and declined to comment further. Ms. Weingarten said the situation exemplifies the school’s strength, arguing that UFT officials treated Ms. John more fairly than the city Department of Education often does.

“I would still put that process into place any time of day compared to what the DOE has in place under Chancellor Klein,” Ms. Weingarten said.

Before being reinstated at the school, Ms. John said the school functions as a “dictatorship” rather than a democracy, as it advertises. She said the UFT’s management only exacerbates the problem.

“It makes it very difficult because, essentially, Ms. Danis’s bosses are the same people who have to represent all of us,” she said.”You don’t really know whose best interests they have at heart. Is it the school? Is it teachers? Is it the students? It’s very hard.”

Ms. John said she was not the only teacher to air concerns; many of her co-workers were polishing their resumes in the hopes of working elsewhere, she said. “It’s a sinking ship. That’s what it is,” she said. “If it continues the way it is, the school will not be able to exist anymore, because everyone’s getting out of there.”

She said an option where teachers were represented by a separate union from the UFT might improve the situation.

This year was not the first time teachers have raised concerns about heavy-handed management.

A former teacher who spoke on condition of anonymity said that she was forced to resign midway through last school year after school officials accused her of having improper credentials to be a public school teacher.

When she left, the teacher said union officials asked her to take a severance package that would include an agreement not to speak to the press about her experience at the school. The teacher refused to take the package. She said she was immediately offered a spot at a Department of Education school after leaving the UFT school, and she is still a public school teacher. Mr. Hickey confirmed that a non-disparagement agreement was part of the package, which he said is not unusual. “This is part of the real world,” he said.

The teacher was part of a larger group that, last school year, raised concerns that the principal was excessively harsh.

Ms. Weingarten said that when she heard the concerns she appointed two UFT officials the task of regularly visiting the school, so that teachers could speak to representatives looking out for the teachers, and the teachers only, as if behind a “Chinese wall” from the school’s management.

“We put a process in place to make sure that the members, the teachers, really felt they had some people that they could talk to confidentially,” Ms. Weingarten said. Ms. Weingarten said that she believes the school’s difficulties do not stem from its unique labor-management structure, but rather from external pressures created by the No Child Left Behind law and the State University of New York, which as part of its oversight of charter schools inquires regularly on progress, including test score gains.

“I think what’s starting to happen is that the focus and fixation on test scores to the exclusion of all else, that SUNY requires, the pressure that people feel from No Child Left Behind, has really stunted good educational opportunity,” Ms. Weingarten said. “And, you know, I’ve seen that in terms of even our teachers and our school leader being really afraid of what the school scores are going to be like. That dominates their life, and instead of looking at it in terms of taking risks, trying new things, and things like that, that’s dominated their life.”

Ms. Danis submitted a resignation letter to Ms. Weingarten Friday, saying this school year will be her last at the school.

In a letter to the school’s board of trustees, the UFT’s charter school coordinator, Jonathan Gyurko, said that Ms. Danis had envisioned making only a three-year commitment when she started the job.

She will return to the job she held before founding the school, at the UFT’s Teacher Center.

The school’s PTA president, Rosa Cribb, said Friday evening that she was shocked by the news of Ms. Danis’s resignation. At a PTA meeting just four days earlier, Ms. Danis had talked with parents extensively about her plans for September, Mrs. Cribb said.

Mr. Gyurko’s letter included a statement from Ms. Weingarten praising Ms. Danis and thanking her for her service.

In an interview earlier in the month, Ms. Danis said the school was progressing smoothly.

“The school is growing, and our students are thriving,” she said.

Ms. Weingarten’s statement also said: “In selecting a new leader, we will search for a candidate committed to the UFT’s goals of student achievement and parent engagement through educator professionalism and voice.”