Some parents of special education students at the Harbor Middle School in Fields Corner are raising concerns about the principal with Boston schools chief Carol Johnson, accusing him of creating a “hostile” environment for their children.

Dr. Robert Martin was installed as principal over the summer as part of a city-wide effort to overhaul underperforming schools. He was put on administrative leave for two and a half weeks this fall a day after a defensive – and widely circulated – e-mail exchange with a parent of a special education student. Boston Public School officials declined to say if the e-mail was the reason for the administrative leave.

Superintendent Johnson met earlier this month with a group of parents to discuss their concerns.

“I can tell you there have definitely been a number of issues around special education at the school,” said Maria Roges, chair of the city-wide Special Education Parent Advisory Council and a parent at the Harbor school.

According to data from the 2008-2009 year, the school has 22 teachers, 267 students, 78 of them with special education status. As one of several schools across the state slated for “turnaround” status in order to improve student achievement gaps, the Harbor Middle School received $1.2 million in federal funding in August.

The Harbor was established in 1998 as a pilot school in the Harbor Point Community Center. According to BPS documents, the school had “fairly acceptable” MCAS scores for the first six years, but struggled with facility issues, high faculty turnover, and administrative changes that caused a “dramatic decline” in the scores starting in 2005.

“We’re committed to all students who attend Boston Public Schools regardless of special needs and academic requirements,” said school department spokesman Matthew Wilder. “We have 12 turnaround schools in Boston and we’ve put in place principals who we feel can really turn around these schools,” he added. “At the Harbor that principal is Dr. Martin.”

In a telephone interview last Thursday before the e-mails were obtained by the Reporter, Martin said he and school staffers were “working around the clock to re-construct the school.” Asked about the abrupt leave, Martin said, “I was out for a few days.”

Martin began his teaching career in 1973 and had served as principal at four Boston-area middle schools before taking the helm of the Harbor Middle School at the start of the 2010 school year. His work at the Hugh R. O’Donnell Elementary School beginning in 2003 earned him accolades from BPS administrators for improving standardized test scores during his tenure. And Harbor Middle School officials say he is making the same strides there.

Asked if there would be any change in leadership at the school, Wilder said, “I can say that at this point — at 12:54 p.m. on Monday — that Dr. Martin is the leader of the Harbor Middle School.”

Roges, who has a 13-year-old special education student at the school, claims there is no process for somebody to fill in when her son’s “one-to-one aide” is out sick. Citing a copy of the school budget she received from the school department’s finance office, Roges charged that the Charles St. middle school has money allocated for special education teachers which has not been spent, and that a “dual teacher model” – where there is a second teacher in the classroom to back up the main teacher of special education students – has not been put in place.

A governance board, necessary for the school to help with parent input on how a certain amount of the discretionary budget is spent, has not been put in place, she added.

“Based on our meeting with the superintendent, we feel our issues have been heard and we are moving forward to address those issues,” said Carolyn Kaine, vice chair of the Special Education Parent Advisory Council.

But Roges said she still has concerns about Martin. “He doesn’t seem to understand his role as a public servant in a taxpayer-funded institution,” she said, adding that she believes he should resign.

Martin was placed on administrative leave on Wed., Oct. 20, a day after he sent a 1,000-plus word e-mail to Roges. He returned on Mon., Nov. 8, Wilder confirmed.

“The issue is there has to be a check and a balance and in these schools there is no check and balance,” said Richard Stutman, head of the Boston Teachers Union, a frequent critic of turnaround schools. “In many turnaround schools, the principal is savvy enough and lacking enough ego to realize it’s a team effort. That’s not the case in every school.”

As a principal, Martin is not a member of the union.

The e-mail exchange appeared to stem from Roges’s concern over her son having to be out of school if his “one-to-one aide” is out sick. On Mon., Oct. 18, Roges complained in an e-mail to several school officials and others that an infrastructure should be available when this happens, at one point informally referring to Martin as “Bob.”

Another school official responded, saying that another aide had been identified to take the sick aide’s place. About 90 minutes later, Martin himself responded with one line: “Who is Bob?”

Roges replied, attaching the e-mail addresses of Superintendent Johnson and others and saying, “Will there be a response to any of the below? Please advise.”

Martin responded the next day to her “recent series of e-mails,” saying he did not appreciate her tone, “self-righteous diatribe or highhanded lecture.” He also said that she was “out of line” for saying the school does not have a plan for a “one-to-one” replacement for her son. They have someone who worked as a special education teacher and is awaiting a certain type of certification, he wrote. “So these hostile and inaccurate accusations the school was unprepared…is just plain untrue,” he wrote in the e-mail. Martin wrote that he hoped Roges was not listening to “certain itinerants” whom he had removed from the school earlier this year because of “poor performance histories and questionable racial attitudes.”

“The reason why the Harbor Pilot Middle School became a Turnaround school is because of the profound incompetence of certain itinerants whose vicious gossip mongering caused irreparable rifts between special education and regular education teachers last year,” he wrote. “I suspect that such an influence may have introduced itself into your rhetoric when you changed my reference from Dr. Martin to ‘Bob.’ When did I become ‘Bob’? I have always referred to and called you Ms. Roges and plan to tolerate nothing else. I am not going to allow you to make either of us your whipping boy (or girl) because to receive [sic] inaccurate information from questionable sources.”

Martin wrote that he stood by what he said. “I will not allow you or anyone else to abuse any member of this faculty by issuing false allegations that cannot be substantiated by facts.”

Roges said Johnson was surprised by the back-and-forth. “After reading the e-mails the superintendent wanted to learn more about what lead up to the exchange,” Wilder, her spokesman, said in an e-mail message.

Asked if Johnson had learned more, or if the matter was ongoing, Wilder said, “That is a personnel matter that we are not at liberty to discuss.”

Martin did not return phone calls from the Reporter this week requesting further comment on the matter.