In the midst of major policy changes intended to make individual schools more accountable for their successes and failures, the city’s schools chancellor, Joel Klein, lost his top instructional leader to retirement.

Deputy Chancellor Carmen Farina, a 40-year veteran of the city’s public school system, announced yesterday that she is stepping down in June to spend more time with her family.

Mr. Klein, a lawyer by training, relied on Ms. Farina to handle instructional issues while he tackled management problems in his sweeping overhaul of the school system.

Yesterday, Mr. Klein called his departing deputy “beloved” and “accomplished.”

“I always thought that it was more than a coincidence that her initials, C.F., are the same initials of Children First,” Mr. Klein said yesterday, referring to the name of his school reforms.

Ms. Farina’s chief of staff, Andres Alonso, will take over as deputy chancellor starting July 1.

Mr. Klein also announced that the head of curriculum, instruction, and professional development, Laura Kotch, 58, would retire at the end of the school year.

The latest change in leadership is one of many since Mayor Bloomberg began restructuring the school system more than three years ago. Many longtime administrators have resigned, retired, or been dismissed.

Ms. Farina, 63, is considered one of the most experienced educators at the education department’s headquarters at Tweed Courthouse.

“Aside from an educator, I am also a wife, a mother, and a grandmother. And this is the time in my life when I can actually spend more time in those capacities,” Ms. Farina said yesterday at Tweed.

“I also want to be able to go on vacation without a Blackberry,” she joked.

Mr. Alonso will be the third person in three years to hold the title of deputy chancellor of teaching and learning.

Unlike his predecessor, Mr. Alonso is not a lifetime educator. After earning a law degree at Harvard University, he took a job at a large New York City law firm.

In 1987, he decided to drop law and took a job teaching special education in Newark, N.J. Eleven years later, he returned to Harvard for the Urban Superintendents Program and to get a doctoral degree in educational administration. He was hired by the education department in 2003.

“I love schools just like I love New York – schools are all about possibility,” Mr. Alonso, who moved to America from his native Cuba at age 12, said.

Educators close to Ms. Farina said that while she did not always see eyeto-eye on issues with Mr. Klein, her retirement was not over any personal disputes.

Ms. Farina came on board just after the city announced a social promotion policy that outraged many educators. She worked to tweak the policy so that elementary and middle school students couldn’t be held back based on the results of a single test. She also was reportedly not happy with recent cuts to professional development for teachers.

Ms. Farina was tapped as deputy chancellor two years ago after her predecessor, Diana Lam, was forced to resign in a nepotism scandal. She was Mr. Klein’s second choice for the job.

Even education experts who disagree with Ms. Farina’s teaching philosophy, especially regarding how to teach reading, said they had tremendous respect for her as a devoted educator.

“While we didn’t always agree with her, particularly on the micromanaging of classroom instruction, she always acted professionally and wanted New York City’s public school children to have the very best education possible,” the president of the United Federation of Teachers, Randi Weingarten, said.

Mr. Klein also announced that his special assistant, Julia Levy, would take over as communications director. Ms. Levy, 26, a former reporter at The New York Sun, will replace Stephen Morello, 59, who is resigning at the end of this school year.