Department of Education announced today that it is moving to close two low-performing charter schools, including one whose network head earned nearly half a million dollars last year and is under investigation by the Attorney General.

The city announced today it would close Williamsburg Charter High School.

One of the schools, Peninsula Preparatory Academy, will close at the end of the year when its charter expires. The 346 students at the school, which has gotten four straight C’s on its city progress reports, will be dispersed among other Far Rockaway elementary schools.

“We have had some struggles but I think the school was definitely on a positive trajectory,” said Ericka Wala, Peninsula Prep’s principal.

The department is taking an even more drastic step with the second school, Williamsburg Charter High School, and revoking its charter midway through the five-year term. Unless the school completely cleans up its management within 30 days, it will close at the end of the year and its students will have to apply to other high schools.

In a letter sent to the chair of WCHS’s board today, the head of the city’s charter schools office, Recy Dunn, paints a picture of massive mismanagement and corruption.

Most of the charges center on founder Eddie Calderon-Melendez, who earned $478,000 last year as the CEO of the Believe Charter Network, which has run Williamsburg and two other high schools.

Citing financial and board improprieties, the city placed the school on probation in September. Chief among the terms of the probation was that the school’s board would sever its relationship with Believe. It did so in November, begrudgingly, but then hired Calderon-Melendez to join the school’s staff earlier this month, according to the letter, which said the school had met just one of 10 probation requirements.

Now, state auditors and Attorney General Eric Schneiderman are investigating the school’s relationship with Believe under Calderon-Melendez’s leadership.

“Despite these ongoing investigations, Mr. Calderon-Melendez continues to have a relationship with the school and the board,” reads the letter. “The board‟s failure to sever this relationship is a serious violation of its obligations under the Charter and state law.”

Two other schools in the network, Southside and Northside charter schools, were authorized by the State Education Department, not the city, so the city cannot shut them down. SED placed both of those schools on probation in October.

At the building that houses Southside and Northside, teachers and staff said this afternoon that they had been instructed by email not to speak to reporters. Asked if he was worried that WCHS’s closure would affect the other Believe schools, Southside’s director of operations, Antonio Serrano said, “No. We are three separate entities.”

Serrano is also the vice-chair of WCHS’s board of trustees, a conflict of interest listed in the city’s letter.

The school’s precarious financial state became clear in 2010 when the owner of the building that it had been renting put the space back on the market, saying that WCHS had not been paying its bills. Previously, we reported that Believe was illicitly sending students to a building that was not permitted for school use.

Revoking a charter is among the most extreme forms of accountability for charter schools and it is a step that the city has taken only once. In 2010, the city closed East New York Prep after documenting failures that the city’s charter schools czar called “the worst in New York that I’ve seen.” In May, state officials revoked the charter of Kingsbridge Innovative Design School after only one year, citing massive mismanagement. The path experienced by Peninsula Prep, where a struggling school is not allowed to stay open when its charter expires, is more common.

“If a charter isn’t coming close to meeting the goals it promised to reach, or is operating in an irresponsible manner, it’s hard to make a case that it should continue to have the privilege of educating students with public money,” said James Merriman, CEO of the New York City Charter School Center, in a statement.

A third school whose future had been in doubt, Opportunity Charter School, got a reprieve today when the department announced it would seek a short-term charter extension — two years, instead of the standard five.

“In our last renewal, we agreed to an accountability plan that would measure our success, and we met those requirements,” CEO Leonard Goldberg said in a statement. “We look forward to continuing to serve as an example of how to meet the needs of this underserved population of students.”

Here’s the letter the city sent to Williamsburg Charter High School’s board chair today: