“She thought we’d had too much change and she didn’t want me to engage in helping change the organization,” he said. “My feeling was that if we were still graduating 50 percent of the students, how could you say we’d had enough change?”

Tensions worsened after Mr. Klein promoted Mr. Nadelstern to lead the effort to bring principal autonomy and accountability to schools across the city. Ms. Fariña increasingly saw her power slip away.

She resigned in 2006, citing a desire to spend time with her family. But she had begun to see her disagreements with the administration as more than just philosophical differences.

“She felt that she was forced out because they were going in a direction that she felt was immoral,” said Dorothy Siegel, a longtime friend.

Ms. Fariña became a critic of the administration’s A-through-F report cards for schools, a practice Mayor de Blasio has promised to end, and she later unsuccessfully opposed an effort to open a charter school in Cobble Hill.

In an interview last week, Ms. Fariña did not elaborate on her differences with the Bloomberg administration but said she was displeased that more resources were not devoted to teacher training. “A lot of decisions were made that were not really thoughtful about how they impacted on classrooms,” Ms. Fariña said.

In recent days, Ms. Fariña has brought that message across the city, promising to place a greater emphasis on the needs of teachers, parents and principals. She has yet to say how she might confront one of the most vexing questions in education today: How do schools weed out ineffective teachers?