Members of the governing board of Greater Egleston High School in Roxbury are demanding reinstatement of their headmaster after the school system placed her on leave amid an investigation into enrollment problems that left more than 100 students locked out of the alternative school this fall.

Dozens of the affected students remain without an assigned school, and the governing board, which conducted its own review over the past month, is blaming the fiasco on the Boston School Department.

For reasons that remain unclear to the governing board, it says, the department dropped from the roster students who had attended last year, and also never formally registered new students who were offered admission by the school in recent months. The board wants the students reenrolled.

“I don’t know what kind of bureaucratic squabble could be so important that it is worth scorching the education of more than 100 kids,’’ Anshul Jain, cochairman of the governing board, said in an interview Thursday. “It is absolutely unconscionable. We need this fixed.’’

The School Department abruptly placed headmaster Julie Coles on administrative leave last week and informed staff that she was under investigation in a letter dated Sept. 20, sparking an outcry at the school she has led for 15 years.

The governing board, in a public statement issued Wednesday, called the removal of Coles and the predicament of students an “unacceptable urgent crisis.’’

The incident marks the second time this year the school system has faced criticism for allegedly pushing students out of an alternative high school.

In the weeks leading up to the new school year, many Dorchester Academy students were left in the lurch after receiving letters that directed them to a school registration site to explore other pathways to graduation. The school system sent those letters after parting ways this summer with a nonprofit that had been running the school, raising questions about Dorchester Academy’s future.

Alternative high schools provide a critical last-chance ­opportunity for many academically struggling students — many of whom are minorities and age 18 or older — to earn diplomas. The upheavals at the two schools come as the school system has been enjoying historic increases in its high school graduation rates, an accomplishment Mayor Martin J. Walsh has been proudly pointing to in his bid for reelection.

In a statement, Superintendent Tommy Chang said he was disappointed that the two governing board cochairs issued their statement amid the investigation. (The cochairwoman is Joanne Allen-Willoughby.)

“As this investigation continues, we are focused on making sure all students who want to be enrolled in the Boston Public Schools are in school and learning,’’ Chang said. “BPS continues to advise any students seeking to enroll at Greater Egleston High School to do so by contacting the BPS Re-Engagement Center, where I have personally spent time meeting with students and staff.

“However, due to the fact that there is an ongoing investigation into recent practices at Greater Egleston, I am unable to comment directly about issues raised at this time,’’ Chang added.

Chang said in his statement that he is trying to work with the board to resolve the issues.

Coles could not be reached for comment Thursday.

Greater Egleston, which educated about 225 students last year, opened two decades ago and operates as a pilot school, giving it freedom from some school system policies, including admission practices. The school requires applicants to be interviewed to make sure they are a good fit, and eventually submits a list of admitted students to the school system to be formally registered.

The school has placed strong emphasis on having students explore and research potential careers, providing opportunities for them to work on relevant internships. And because many students work full-time jobs to help support their families, the school has given them flexibility to take online courses outside traditional school hours.

The board is planning to host a community meeting Tuesday at 7:30 p.m. at the school to gather additional information from those directly affected, and it plans to present a comprehensive report to the Boston School Committee the following day.

So far, the board has assembled a fairly detailed chronology of events.

According to the statement, the school’s administration discovered on Aug. 28 that more than 100 students were not on the school’s roster, prompting administrators to notify students about the problem. The School Department, according to the statement, never provided an explanation to the school or to the students about “why they were disenrolled.’’

Coles and other administrators then pressed the school system to reenroll the students and collected documentation at the School Department’s request to help with reenrollment, but the School Department never responded when the school repeatedly notified them that the information was ready.

Then on Sept. 13, one of the school system’s registration offices informed the school that it had been instructed to reject new enrollments, according to the statement.

Some students showed up to school on Sept. 18 but were told they were not enrolled, according to the Bay State Banner. Two days later, the school system issued the letter to staff about Coles’s administrative leave, and the board said in its statement that the school system provided Coles “with no substantive justification.’’

“From Aug. 28 onwards, Ms. Coles relentlessly advocated for the reenrollment of these 100+ students,’’ the board’s statement said. “Her longstanding advocacy for a consistently underserved cohort of students — overwhelmingly of color and overwhelmingly subjected to a host of structural and institutional obstacles — is now further undermined by these events.’’

The school system’s reengagement center is working with students as quickly as it can to get them reenrolled at the school, but some students have not responded to inquiries from the center, said Neil Sullivan, executive director of the Boston Private Industry Council, a nonprofit that helps run the reengagement center.

“We are doing our best to get the situation under control, and we are moving in the right direction,’’ Sullivan said.

James Vaznis can be reached at james.vaznis@globe.com. Follow him on Twitter @globevaznis.