The superintendent of Swampscott Public Schools announced Thursday that she will not renew the contract of an elementary school principal who recently came out as transgender and who will remain on paid administrative leave for the rest of the school year.

In an e-mail to the community, Superintendent Pamela Angelakis said she informed principal Shannon Daniels of the decision earlier this week. Daniels’ contract does not expire until June 30, but the district had to notify Daniels by March 15 if the contract was not going to be renewed.

Angelakis did not specify a reason for not renewing the contract for Daniels, who has been on leave for more than two weeks.

“As this is a personnel matter, and out of respect for principal Daniels’ privacy, I will not be commenting on the reasons for this decision,’’ Angelakis wrote in the e-mail. “Swampscott Public Schools wishes principal Daniels the best moving forward.’’

The news capped a tumultuous month at Stanley Elementary School, since the Feb. 6 announcement that Daniels would begin presenting as a woman. While many supported the principal in the transition, some parents bristled at the suddenness and faulted the administration for seeming to prioritize Daniels’ concerns over those of students.

At a meeting held to inform parents about the changes on Feb. 12, some of them brought up issues with Daniels’ record, citing grievances brought by teachers. Two even went so far as to question whether the transition was being made to protect Daniels’ position and whether a transgender principal would be in a “protected class’’ and could not be replaced.

Angelakis, who declined to discuss personnel issues that night, fiercely pushed back at such assertions. But parents also questioned her leadership in a time of upheaval and Daniels’ willingness to participate in interviews with The Boston Globe and other news outlets.

On March 1, a group of parents gave the School Committee a letter they deemed a vote of “no confidence’’ in Daniels, pointing to issues that predated the transition, and the distraction it caused.

“Throughout the past few school years, many concerns have been raised regarding Ms. Daniels’ leadership, specifically regarding trust, collaboration, decision-making, and communication with staff and families,’’ the parents wrote. “We also believe that Ms. Daniels has failed to present a proper learning environment and has not put the safety of our children/students first. We believe that all students will succeed in a climate that fosters a passion for learning, one where they will not be interrupted by outside factors that have a negative impact on their learning environment.’’

The petition also faulted Daniels for creating a “toxic environment for both students and staff,’’ being unwilling to listen, and for delayed or incomplete communication. “We need a different, more solid leadership,’’ the parents wrote. “The morale is too low, and it is time for a change.’’

Amy O’Connor, chairwoman of the Swampscott School Committee, said last week that about 70 members of the community signed the petition, although some of them did not have children at Stanley. But she also noted that hiring decisions were the purview of the superintendent, not the School Committee.

Reached on Thursday, O’Connor declined to speak to specifics but said the decision not to renew Daniels’ contract was not driven by the parents’ vote of no-confidence.

“That did not influence the superintendent,’’ she said.

The news came at a difficult time for Stanley Elementary School, which is also facing teacher cuts and a restructuring that will require many students to transfer to other elementary buildings. Many parents had complained about the abrupt announcement of the principal’s transition on a Tuesday afternoon, noting they had to immediately figure out how to explain the situation to their children, none of whom are older than fourth grade.

But people often raise concerns about “distractions’’ or “discomfort’’ when a transgender person is transitioning, Jeff Perrotti, the director of the Massachusetts Safe Schools Program for LGBTQ Students, told parents at the Feb. 12 meeting.

“Discomfort is not a reason to treat people inequitably,’’ he said.

Still in a separate interview, Perrotti acknowledged, “I don’t think it’s unreasonable or patently discriminatory to say, ‘let’s talk about how the timing makes the most sense.’ ’’

Stephanie Ebbert can be reached at ebbert@globe.com. Follow her on Twitter @StephanieEbbert. James Vaznis can be reached at james.vaznis@globe.com. Follow him on Twitter@globevaznis.