A Brooklyn charter school that has the dubious distinction of committing the worst charter violations city officials say they’ve ever seen is about to be closed.

New York City rarely closes charter schools, but yesterday Department of Education officials told East New York Preparatory that it intends to revoke the school’s charter when the current school year ends in June. The K-4 school was authorized by Chancellor Joel Klein in 2006 and would only be the fourth charter school in the city to close.

Director of the city’s office of charter schools, Michael Duffy, said DOE officials began noticing problems last year when parents contacted the department and the school was put on probation in February.

“It’s certainly the worst in New York City that I’ve seen,” Duffy said.

Rather than using its probationary period to turn around, the school’s problems seemed to multiply, Duffy said. Its founding principal, Sheila Joseph, is accused of inflating her salary from $120,000 to $180,000, which she could easily do as vice chair of the school’s board of trustees. According to the DOE’s charter revocation notice, Joseph had Mercer Givhan, the father of her child, placed on the board, which DOE officials said put the board’s independence in doubt. He was paid $5,500 that the school cannot explain.

Last year, a review by the State Education Department found that 48 East New York Prep students were discharged before the state’s standardized tests were given. Among the students who left were seven low-scoring third-graders. That same year, 86 percent of the school’s students scored proficient in English and 100 percent were proficient in math.

An review conducted in 2007 noted that “the percentage of special education students is much lower than in other schools,” and that there were no English Language Learners enrolled.

The school’s teacher turnover has also been extreme. Between June of last year and September of this year, East New York Prep lost every teacher it had, Duffy said. In their stead came new teachers, most of whom are in Teach for America.

It’s not clear whether teachers left voluntarily or were fired. Joseph did not return calls for comment.

The school’s board has 30 days to respond to the DOE’s accusations and then Klein will make a final decision. Duffy said the department plans to hold a public meeting at the school on February 3 to explain the closure to parents and to offer help getting students placed into other schools or entered into other charter schools’ lotteries.