The weary tone of John McDonough's voice said as much as the bleak facts of the story he told last night. The Boston Public Schools' chief financial officer spoke in little more than a whisper as he described the implications of a $63 million budget deficit projected for the beginning of next school year.

His report before the Boston School Committee boiled down to two unappealing choices: restructuring resources (likely, the closing of several schools) or sweeping cuts at all schools.

"This is an extraordinarily important time in our history," he said while addressing the committee before an audience of about 75 people at the schools' headquarters on Court Street, next to City Hall. "The decisions you make over the next several months will determine the fiscal stability of Boston schools for years to come."

But Superintendent Carol R. Johnson's words implied she was already leaning toward the first option.

"Restructure our resources strategically in a way that puts students and academic improvement first, or make across-the-board cuts that may jeopardize the progress we have made," read the introduction she issued before McDonough's report.

The rising costs of running the schools and the economic downturn led to the shortfall, McDonough said, citing similar problems during the prior two years, when the BPS eliminated 771 jobs, implemented wage freezes for managers and principals, and closed six schools.

Despite the gloomy financial picture, some schools and programs have thrived. Arts and music classes took on 3,000 additional students and there were sharp increases in the numbers of students taking Algebra I in eighth grade and taking advanced placement classes, McDonough said.

Increased efficiency is critical to continued progress, he said, pointing to the example of 5,600 empty seats in Boston schools, costing the system $25.2 million per year.

Many of the audience members were parents of students enrolled at schools rumored to be candidates for closures.

"[My children] are in an environment that's incredible. I don't want to send them to a school with 800 students," said Jenna Brown, mother of two pupils at Roger Clap Elementary School in Dorchester, during the committee's public comment period. "You guys have an aerial perspective instead of an idea of what's happening on the ground. How are you helping me by dispersing my children and spreading them around the community?"

Johnson had anticipated the reaction from the public when she had explained earlier in the meeting the dilemma faced by the School Committee.

"People think that Mayor Menino can wave a wand and the $63-million will disappear," said Johnson. "These are very tough choices. I don't expect we can all agree. It's a problem that belongs to the entire city of Boston and we have to work collectively to come up with solutions."

School administrators will present specific recommendations at a Dec. 2 meeting and the School Committee will vote on possible school closures at its Dec. 15 meeting.

Anti-bullying plan is still taking shape

The School Committee also listened to a brief presentation of key elements of a bullying prevention and intervention plan.

Former Brook Farm School headmaster Ed Donnelly, who is leading the anti-bullying initiative, listed steps taken since state legislators passed a measure in May requiring all school districts in the state to submit formal plans by the end of the year to counter bullying behavior in schools.

Among the BPS actions have been the hiring of a consultant to work on the Bully Prevention and Intervention Initiative and updating technology guidelines with strictures against cyber-bullying, Donnelly said.

Other components of the under-development proposal include professional development for all BPS employees — including bus drivers and cafeteria workers, as well as teachers; a program aimed at modifying the behavior of bullies; and parent workshops.

"We need to do a better job of tracking data, school to school," said Johnson. "Repeated suspensions don't necessarily work. We don't always have family support for that. We have a lot of work to codify that."

Donnelly will submit final plans to the committee in early December and the school committee will vote on the proposal at its Dec. 15 meeting, said chair Rev. Gregory G. Groover, Sr.