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The School Committee on Wednesday night approved an annual budget that for the first time exceeds $1 billion, but the spending plan nevertheless calls for wide-ranging cuts, from closing two schools to eliminating more than 130 central office positions.

The two schools slated for closure, an elementary school and a middle school both located in Hyde Park, will hold their last classes in June, ending tumultuous times for each. The Elihu Greenwood Leadership Academy has been teetering on the brink of state receivership for years, and Rogers Middle School has been plagued by low enrollment and poor achievement.

The Rogers building will not remain empty for long. Interim Superintendent John McDonough said the Muniz Academy in Jamaica Plain will probably relocate there in 2016 after renovations are completed.

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Michael O’Neill, the School Committee chairman, said the cuts reflect a “very, very challenging” financial situation that the district faces as the growth in expenditures far outpaces increases in revenue.

But the Citywide Parents Council urged members to reject the closures, arguing it was premature to close any school before the district finishes its master plan for facilities.

“We find it inequitable that Hyde Park is losing two schools,” Barbara Rosa, one of the parents council’s co-chairs, said in testimony before the vote.

The meeting was a more low-key affair than other budget votes in previous years, when budget-cut protesters would march around the School Department headquarters singing civil-rights-era songs while banging drums and blowing horns. The $1.01 billion budget was unanimously passed by the committee.

Wednesday night’s subdued atmosphere was probably due to McDonough’s decision last week to give West Roxbury Academy a one-year reprieve from closure. The most vocal protests had been coming from students and staff from that school.

McDonough also backed away from closing Community Academy, a high school in Jamaica Plain that specializes in teaching academically struggling students. That school will absorb Middle School Academy, another alternative program that works with students with behavioral issues.

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An outside organization will probably oversee that program as part of the merger, raising concerns from some members of the public.

Miren Uriarte, a school board member, also expressed displeasure that the budget proposal called for an outside provider, saying it was a policy issue that should have been considered separate from the budget. More broadly, she criticized the budget process this year as “very haphazard.”

Overall, the $1 billion in spending is up by about 4 percent over this year’s amount, but the cost of doing business is rising faster than revenue. The rising costs include contractually negotiated pay raises and new initiatives, such as extending the day at more than a dozen schools next year and adding more prekindergarten seats.

The reductions in central office staff are the second round of staffing cuts in that area in little more than a year.

Some students from Madison Park Technical Vocational High School in Roxbury, where the quality of education has long been a concern, made one last unsuccessful attempt Wednesday to persuade the committee not to cut $1.5 million from its budget next year.

“We need the money,” said Adrian Perez, a 10th-grader, in testimony. “We are the only vo-tech school in Boston. We should be one of the top schools in the city. That’s what was promised to us and that promise is not being kept.”

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James Vaznis can be reached at jvaznis@globe.com. Follow him on Twitter @globevaznis.