The Prince George’s County school board unanimously approved a $1.6 billion budget early Tuesday that would cut as many as 700 teaching positions in the coming school year but preserve some transportation and education programs that residents had pleaded to be saved.

The vote, just after midnight, capped a five-hour meeting in which board members debated the costs and benefits of several initiatives in Maryland's second-largest school system.

In one key action, the board sought to maintain staffing at a popular science center in Lanham by limiting funding for a new project with Prince George’s Community College.

The project, known as “middle college,” will begin in the fall with a group of 100 high school freshmen taking classes at the community college. Transportation costs for the program were initially estimated at more than $1 million.

But the board accepted a proposal by member Carolyn M. Boston (District 6) and Vice Chairman Donna Hathaway Beck (District 9) to limit funding to $1,900 per student — the average cost for busing to other specialty and magnet programs. That action freed up money to keep the 12-member teaching corps at Howard B. Owens Science Center, which serves 32,000 students annually.

In the budget debate, several board members took a stand against investing in new programs when current programs were being axed. For example, the board turned down a proposal to expand a Chinese immersion program at Paint Branch Elementary School College Park in partnership with the University of Maryland.

The school board’s approval was the last major action in the budget season. The County Council still must approve the budget, but that is expected to be a formality.

Spending in the fiscal 2012 budget would be down 2 percent from the year that ends June 30. The school system has slashed spending steadily since 2008 in response to declining property tax revenue and dwindling enrollment.

In that time, the number of students has fallen nearly 5,000, to a projected 125,000 in the next school year. More than 3,000 jobs have been cut in that period, about half of them teaching positions.

Under the budget, Prince George’s schools would also lose nearly 100 librarian positions and reduce hours for athletic directors. Average class sizes would increase by one student in most grades.

Officials are trying to prevent layoffs by offering a retirement package to veteran employees and eliminating vacant positions. Nearly 550 workers, from teachers to bus drivers, have applied for the package.

The final layoff tally won’t be available until later this summer, but school system spokesman Briant Coleman said Tuesday afternoon that about 200 teachers will lose their jobs.

The budget ends several months of public debate and political wrangling. Superintendent William R. Hite Jr. proposed cutting several popular programs, including the ecology learning center Camp Schmidt near Brandywine and an initiative for students falling behind in reading skills.

Hite also proposed no longer busing students to magnet schools, long seen as a way to ensure socioeconomic diversity in the county system. Those and other cuts he proposed were meant to help close a $155 million budget gap.

In February, the school board begrudgingly passed the Hite plan with the intention of pressuring the county and state to provide more money. The tactic appeared to pay off somewhat. The state and county provided an additional $10 million, enough to save the magnet school busing and Camp Schmidt as well as to retool the reading program.

Other initiatives were not spared. Early-education programs will be reduced to a half-day. Students who participate in high school sports will have to pay a $50 fee or seek a needs-based waiver.

The school system is far from alone in facing serious cuts. Montgomery County schools are cutting about 600 positions, including 34 librarians and 51 staff development teachers, although the system expects enrollment to climb by 3,300 students in the fall. In the past four years, Montgomery schools have lost nearly 1,300 positions.

Prince George’s school board members said the voted for the budget reluctantly.

“It is outrageous that we have to struggle with this,” said board member Rosalind A. Johnson (District 1). “No matter what, it’s robbing Peter to pay Paul. So we’ve just got to get moving.”