ALBANY — The Brighter Choice Foundation is in danger of losing two of the 11 charter schools it supports in the city.

The state agency overseeing the schools said Albany Preparatory Charter School is closing for poor academic performance, not to strengthen it.

School officials told parents they were "merging" Albany Prep with the Achievement Academy Charter School. That allowed school and Brighter Choice officials to avoid the stigma of closure. Parents were told it was a move to strengthen each school and to avoid keeping two school administrations.

In a letter sent to parents last week, SUNY Charter Schools Institute interim executive director Susan Miller Barker said the school will be closed by its own Board of Trustees because they thought it would be shut down by the state.

Because it is not merging with another school as parents were led to believe, students are not guaranteed seats and must reapply for admission.

The Achievement Academy is also at risk of closure because of poor academic performance and enrollment issues. The school may be shut down after the next school year if it does not turn around, according to the letter.

"In order for Achievement Academy to continue teaching students beyond June 2013, it must prove it provides a strong academic program for all students," Barker wrote.

In 2010, both Albany Prep and Achievement Academy were flagged for poor academic and economic performance by the State University of New York and given three-year charter renewals instead of the usual five-year renewals awarded to healthy schools.

School officials continue to offer their own interpretation of its demise.

Albany Prep Board Chairman Brian Backstrom said the school was not being closed, but instead voluntarily returning its charter to avoid a fight over closure.

"It is a cessation of operations so the process can be easier for our students, our parents and for the charter community in Albany," he said.

He said the Charter Schools Institute's letter to parents was "completely unfounded" and caused unnecessary confusion among parents of both schools. Backstrom said it was merely a dispute over legal terminology, though he acknowledged that students from Albany Prep would have to apply for admittance to Achievement Academy. More than 200 students currently attend each of the two schools, but Backstrom has said the newly configured Achievement Academy, for grades five through eight, will only have seats for about 300 students.

Backstrom said he expected Albany Prep will soon post improved student test scores that will show its performance has been turned around.

Nonetheless, the board is returning the charter because "they wanted us to hit a home run and we hit a triple," Backstrom said.

The Brighter Choice Foundation supports 11 charter schools in Albany, which educate about 2,500 students. The district will send $35 million of its $208 million budget to charter schools next year.

The charter schools will need a fleet of moving vans this summer as multiple schools switch buildings. The strongest school, Albany Community Charter, will be split between two buildings, both owned by the Brighter Choice Foundation. The weakest charter school, Albany Achievement, will move from a Brighter Choice-owned building to a rental building at 75 Park Ave.

The shuffling of buildings raises serious questions about the future of Achievement Academy, Albany schools spokesman Ron Lesko said.

"If Brighter Choice thought Achievement Academy was going to be around to pay its bills, they would have not evicted them," he said. "These schools are not living up to the promises they made to families."

swaldman@timesunion.com • 518-454-5080 • @518Schools