A majority of teachers are leaving two of the city’s lowest-performing schools, where they were forced this year to reapply for their jobs, according to data released Wednesday.

At long-struggling Boys and Girls High School in Bedford-Stuyvesant, Brooklyn, 40 of 54 teachers — or 74 percent — are not returning next year, according to the city. At Automotive High School in Greenpoint, Brooklyn, 24 of 38 teachers are leaving, or 63 percent. At Boys and Girls, half of the departing teachers re-interviewed for their jobs but were not rehired, while at Automotive all but three of the teachers who are leaving chose not to reapply for their positions.

The schools’ rehiring process has attracted great interest partly because they are the most high-profile members of the city’s “Renewal” improvement program, in which the de Blasio administration is investing more than $538 million over the next three years to try to overhaul 94 under-performing schools. But the process itself was also highly unusual, a restaffing scheme ordered by the state and agreed to by both the teachers and principals unions, which some doubted would lead to the steep turnover that resulted.

It is not entirely surprising that so many teachers chose to leave.

Both schools are under intense state pressure to improve, and could be closed if they fall short. Also, staffers at both schools said some teachers had clashed with their principals, who have a mandate to make major changes. And if the teachers were already considering a move, they were likely emboldened by a guarantee that the the city will place them in other Brooklyn high schools if they fail to find new jobs — a stipulation of the city-union deal that led to the rehiring process.

The schools’ slumping enrollment numbers may have also created a need for fewer teachers. And the principals may have used the rehiring process as an opportunity to pressure some teachers not to return.

The high turnover comes as Chancellor Carmen Fariña has called on principals to try to retain teachers who are committed to their jobs even if they need more training, but encouraged them to urge teachers deemed incapable of the work to leave. Education department officials said that a portion of the teachers who did not reapply were “counseled out,” but a few people familiar with the rehiring process said teachers had made their decisions freely.

In a statement, Fariña said the hiring process had been collaborative, but added that turning around troubled schools requires tough decisions.

“Schools need to have the right leadership, the right teachers, and the right school staff to raise student achievement,” she said.

The Bloomberg administration attempted similar shakeups at two dozen bottom-ranked schools in 2012 (including Automotive), but was ultimately blocked after a legal battle with the teachers union. In this instance, the union agreed to have its members reapply for their jobs, but with the important difference that it would help make the rehiring decisions and that rejected teachers would be guaranteed new placements.

“The process allowed teachers to have a voice,” United Federation of Teachers spokeswoman Alison Gendar said in a statement, “and created a way for staff members to decide if their skills were a good fit for these new plans, or if they were better suited to serve the district’s students in a different program.”

When the re-staffing plans were announced, critics suspected that the joint city-union hiring committees at each school would not spur the dramatic staff overhaul they said was needed. In November, State Board of Regents Chancellor Merryl Tisch commended both sides for agreeing to the plan, but said she did not want to see “two teachers who were going to retire anyhow retiring.”

The numbers announced Wednesday seemed to appease some of the critics. The pro-charter school group StudentsFirstNY, which has attacked the de Blasio administration for doing too little to revamp the city’s struggling schools, called the turnover “a good first step.”

The state has not ordered the other Renewal schools to enact a similar rehiring process, and the city-union deal does not extend to them. However, city officials have said the process could serve as a model for those schools.

Now that it is clear a large number of teachers is leaving each school, officials said they will help each principal find qualified replacements. At the same time, the principals will have to manage any fallout from the turnover, which has the potential to destabilize schools already in the midst of major changes.

A teacher who chose not to reapply to Automotive said he doubted that many experienced educators would opt to work at a school facing such scrutiny, where teachers must come in for extra training this summer and will be expected to quickly boost their students’ performance. He added that several of his students had already told him they were dreading the turnover.

“One said, ‘We’re going to give these new teachers hell,’” he said, adding that the turnover is “going to have an adverse effect, without a doubt.”

However, Tisch and state education department officials have said such a shakeup is just what these schools needed.

The officials last year labeled both schools “out of time” to make major improvements, including raising their strikingly low graduation rates. They demanded that the city take drastic steps to revamp the schools, and required that any “unwilling or ineffective” personnel be replaced.

In response, the city and unions formed a plan that established hiring panels made up of city and union representatives, along with parents. The panels opted to rehire the principals, who then joined in the staff hiring decisions.

At Boys and Girls, 14 of the 34 teachers who reapplied for their jobs, or 41 percent, were brought back. At Automotive, 14 of 17 reapplying teachers, or 82 percent, were brought back. The deal allowed the panels to rehire as many or as few staffers as they chose.

Two Boys and Girls teachers said they chose not to reapply because they objected to the leadership style of the new principal, Michael Wiltshire, who was recruited from a high-performing Brooklyn school. They said teachers who were not retained were called to Wiltshire’s office over a loudspeaker on the last afternoon of school and handed letters with news.

Wiltshire did not immediately respond to an email. But in a statement that officials sent reporters, he said, “I’m proud of the progress we’ve made so far, and the staff we’ll have this fall will be the right team to best support students.”

The teacher who did not reapply to Automotive said the assurance of a placement in another high school offered “a little bit of insurance” as he looks for a new school. He called Principal Caterina Lafergola a demanding and skilled leader, but said she had butted heads with a faction of Automotive teachers.

Lafergola declined to comment. In a statement sent to reporters, she said, “This is going to make a real difference, and will help ensure we have the right staff in place to best support students.”

Both principals are now trying to replace some of the teachers who left. An education department spokeswoman said the city will help organize two recruitment events at each school this summer. And like all of the Renewal schools, they will each get $27,500 to offer large bonuses to veteran teachers who agree to coach other teachers.

It is likely that both schools will not replace some of the departing teachers. Each has hemorrhaged hundreds of students in recent years. Boys and Girls, for instance, has seen its enrollment plunge from 2,300 in 2010 to under 500 students today. While officials say that applications there are up, a teacher said last month that only 65 freshmen had enrolled.