Three years after stepping in to save a Woodbury arts and science magnet school, the Perpich Center for Arts Education is under fire for its management of the school, and on Thursday its board chairman stepped down unexpectedly.

Pierce McNally, an attorney and a board member for the past five years, attributed his decision to “a recent confluence of occupational, personal and professional opportunities and obligations,” according to a Minnesota Public Radio report.

His departure comes as the state-run agency awaits results of a legislative audit inspired in part by parental concerns as well as student and staff turnover at Woodbury’s Crosswinds School, a grades 6-10 facility with a stated mission of helping all students achieve by teaching in and through the arts.

State Rep. JoAnn Ward, DFL-Woodbury, who pushed for the program audit, said in a news release earlier this year that she had heard from “many parents, faculty and community members who have grown dissatisfied and question whether Perpich is truly fulfilling its educational mission.”

The Perpich Center took over management of Crosswinds in 2013 after the East Metro Integration District, a multidistrict collaborative promoting the integration of students in St. Paul and its suburbs, decided it no longer could afford to run Crosswinds and Harambee Community School in Maplewood.

Harambee now is part of the Rose­ville School District.

Crosswinds parents endorsed the Perpich Center plan, and the agency described the Crosswinds program as a strong fit with its own commitment to seeing students of diverse backgrounds transformed through the arts and global and cultural awareness.

Since then, however, Ward said she has heard concerns about the elimination of parent groups, cuts in art education experts and inconsistent direction to faculty members. She also questions whether the board cedes too much authority to the executive director, saying it raises accountability concerns.

In addition to the legislative audit, the Perpich Center board has formed its own task force to look into complaints aired during a summer listening session at the school. The group is exploring issues relating to financial transparency, communication, board responsibilities, and enrollment and retention.

McNally was not a task force member. He declined to comment on Friday.

Earlier this year, Legislative Auditor Jim Nobles sent a letter to Sue Mackert, executive director of the Perpich Center, seeking the release of information that his office had requested, adding that a failure to do so would make her “noncompliant with state law.”

The center fulfilled the request, a spokeswoman said Friday.

The Office of the Legislative Auditor has yet to present its findings regarding the program/governance audit to the Perpich Center.

The office also is conducting a financial audit of the agency.

The Perpich Center is known primarily for its arts high school in Golden Valley. The agency has a board of directors appointed by the governor, and an annual budget of about $8 million.