District charter schools had fewer financial problems in fiscal 2012 compared to the year before, according to a report released Wednesday by two city agencies and the D.C. Public Charter School Board.

The study, based on an examination of schools’ annual financial audits, is meant to help identify and address fiscal weaknesses before they mushroom into problems that force a school to shut its doors.

It flagged three charters for poor fiscal performance during the year ending June 30, 2012, down from 13 the year before.

D.C. Bilingual, a Columbia Heights elementary school, had an operating deficit of more than $600,000, raising questions about its long-term viability, according to the charter board.

Myrna Peralta — president of CentroNia, the organization that operates D.C. Bilingual — said she is confident of the school’s continued viability. But she acknowledged that the operating deficit, driven in part by the expense of serving a growing number of high-needs special education students, is a problem.

The school has reduced staffing costs by employing fewer adults in each classroom, she said, and is looking for ways to reduce the cost of special-education services without sacrificing quality.

“Our financials will be much better” in fiscal 2013, she said, estimating that the school will reduce its operating deficit by more than half. Scott Pearson, executive director of the charter board, agreed that the school’s financial position has improved enough in recent months to allay the board’s concerns.

Officials at National Collegiate Preparatory, a high school in Southeast Washington, also said they have improved their fiscal picture in 2013 after spending heavily in 2012 to establish an International Baccalaureate program. “We are a school that's going to be here for a long time to come,” said Executive Director Jennifer Ross.

The school operated at a deficit in fiscal 2012 and had low liquidity, with enough cash on hand to cover only one day of operating expenses. The charter board recommends having at least 30 days of cash on hand; the median charter school in 2012 had 59 days of cash on hand.

Ideal Academy, an elementary and middle school in the Lamond-Riggs neighborhood in Northwest Washington, also had only one day’s cash on hand, and charter board officials expressed concern about the school’s long-term viability.

A school employee said Tuesday that the principal was out of town and unavailable to comment on the report. The charter board decided to close Ideal’s high school campus in 2011 due to poor academic performance.

The city’s 53 charters in fiscal 2012 reported total revenues of $614 million, up 15 percent from the year before and up 27 percent since 2010.

The new report — authored by the charter board, the Office of the Chief Financial Officer and the Office of the State Superintendent of Education — includes a separate two-page financial snapshot of each charter school.