SALEM — Problems at the Bentley Academy Charter School continue.

Justin Vernon, the headmaster who helped the struggling K-5 school in Salem transition to charter status, resigned in May after a complaint to the Department of Children and Families was filed against him.

While a DCF spokesman declined to confirm whether an investigation is ongoing, the school’s board of trustees said in a prepared statement that the complaint was filed May 5. The board is in the process of “thoroughly reviewing the school’s policies and procedures regarding student discipline,’’ the statement said. “We take this investigation seriously.’’

Bentley has been one of the lowest performing schools in the state for years. It has been designated at Level 4 since 2011, one classification shy of being taken over by a receiver.

Vernon, who worked at the school for two years, was placed on paid administrative leave after the complaint was filed. Kelley Rice, a spokeswoman for the Salem public schools, said Vernon resigned on May 20.

Rice declined to comment on why Vernon had been placed on administrative leave. The Salem Police Department said it did not have a police record related to any incident at the school.

In February, Vernon announced plans to leave the school at the end of the academic year. In a statement issued after he resigned, he called the allegations untrue.

“The basis for the allegation of neglect was patently false,’’ he said. “I am aware that a report was made and the validity of that report is currently under formal review. I am confident that my strong reputation as an educator will speak for itself.’’

In 2014, Salem hired an outside contractor — the Blueprint Schools Network— to help boost student achievement by managing the school and introducing a new curriculum. That fall, it opened with a new set of educators. The previous 16 teachers were either reassigned to other schools or fired.

The school, which has a long history of low MCAS scores, changed its named to the Bentley Academy Charter School and obtained a Horace Mann charter in February 2015. It also appointed an independent board of trustees to help run the school.

But it is unclear how much of an impact the new system has made. The school’s combined MCAS scores in English, math, and science from 2015 lagged behind the Salem district and the state average, with a majority of the students designated in the “needs improvement’’ and “warning/failing’’ categories.

In its school accountability study, the Department of Elementary and Secondary Education reported that the Bentley had successfully “met target’’ for Hispanic-Latino and English language learners, but did not meet its overall target for all students, including its high-needs learners.

When compared with similar schools, the Bentley ranked in the lowest 7 percent statewide in 2014. While its overall school performance ranking jumped to the 13th percentile in 2015, that was not enough to shake its Level 4 status.

During this past school year, 75 percent of the 254 students who enrolled in the school were classified by the state as high-needs learners.

Mayor Kim Driscoll, who also heads the Salem School Committee, did not respond to an interview request.

Meanwhile, Bentley’s board of trustees has named Marlena Afonso as the new head of school. Afonso previously served as the school’s dean of curriculum.

Steven A. Rosenberg can be reached at srosenberg@globe. com.