The top financial leader of San Diego Unified will resign at the end of June; the school board accepted his resignation letter behind closed doors tonight. He will continue to be paid his roughly $155,000 salary until then, working on unspecified “special projects” for the school district.

Chief Financial Officer James Masias has been on paid administrative leave since March 25. School district officials have declined to talk about why, though school board President Richard Barrera has repeatedly stated that it has nothing to do with the credibility of Masias’ budget work.

Interim Superintendent Bill Kowba has not yet decided what special projects Masias will take on. School officials said Masias will work off site, not at the school district offices on Normal Street.

Former employees from the budget department declined to talk about Masias’ performance as a boss. Numerous finance workers left the school district while Masias was there, some taking a bonus that encouraged veteran employees to leave. One former employee said the stress of working long hours and facing constant demands from the school board and former superintendent drove him away.

“I don’t know if that’s what caused James’ stress level to rise or not, but there was definitely a lot of stress there,” said Ken Leighton, the former controller, who now works as the executive director of fiscal services for Grossmont schools. He recalled that he once worked 36 hours straight in one night. “[Masias] never created an unpleasant environment for me. But you could see that he was under stress.”

Barrera said that stress was another unfortunate but necessary byproduct of the ongoing financial crunch for California schools, which have now faced budget cuts three years in a row.

“Is it better that the stress is felt more strongly here” — in the central office — “or out in the schools?” Barrera asked.

That stress may get a little lighter: Kowba said one advantage of the planned reorganization of its central offices is that the finance chief will be able to focus on budgets and budgets alone, not other services like transportation and maintenance.

While the school district searches for a new finance chief, its interim special projects chief Phil Stover will oversee the department. There is still plenty of work for the budget department to do this spring as San Diego Unified adjusts and finalizes its budget for next school year, but Kowba said he is confident that the budget team can handle it.

— EMILY ALPERT

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