The City Council and the head of the principals union have urged the Department of Education to save money by reducing the number of new schools it opens this fall. But the department appears not to be laying the groundwork to adopt that strategy, instead announcing today its plan to close a large Manhattan high school.

Bayard Rustin High School for Humanities will not accept any new ninth-graders for this fall and will close permanently when its last students graduate in 2012, the DOE told staff there yesterday. The school, which currently has more than 1,500 students, has struggled mightily in recent years. Its graduation rate is below 50 percent, and it received an F on its 2007-2008 progress report, the tool the city uses to evaluate schools.

The school’s closure comes after recent turmoil that included a spike in teacher turnover and an investigation into whether the school had tampered with Regents scores.A long article that appeared in the Chelsea Now newspaper in May described high teacher turnover, a low graduation rate, and disorganization in the school’s structure after it was reconfigured into small learning communities. In the article, parents and teachers said they were concerned that the Bayard Rustin’s sizable populations of overage students, students with special needs, and English language learners were not being adequately served.

The principal tasked with dividing the school into small learning communities, John Angelet, announced his resignation this spring. The Post reported in May that under Angelet’s leadership, the school had been investigated for tampering with Regents scores. Angelet’s replacement, Nancy Amling, came to the school from the Queens High School of Teaching.

According to a DOE spokeswoman, Bayard Rustin’s building on West 18th Street will eventually be home to five or six schools. This fall, she said, at least one new school will open in the building. Two popular small high schools that accept transfer students, Humanities Prep and the James Baldwin School, are already open in the building.

Bayard Rustin is the first stand-alone high school to be closed this year. Last month, the DOE announced that the Agnes Humphrey School for Leadership in Red Hook, Brooklyn, a K-12 school, will close at the end of the year.