“Why is he giving you all these gifts? It’s not Christmas,” her mother recalled asking. She followed her daughter into a bedroom and stayed until her daughter told her everything, she said.

The next day, Ms. Pacheco said, she called the school. She said she spoke to Santos Martinez, a staff member, and asked to speak with Dave Levin, one of KIPP’s founders. Ms. Pacheco said she had told Mr. Martinez that the teacher was being “fresh” with her daughter and that he shouldn’t be allowed in the school. She called again the next day and spoke with Mr. Martinez again. He told her he would take care of it, she said.

Her daughter said she had told another school administrator shortly after: Mr. Levin. She said that they were standing in a hallway at the school and that Mr. Levin told her she should never speak with the teacher again.

The Debevoise report disputed that, and it found no evidence that senior leadership had known until 2017. “Each of the individuals alleged to have known about the abuse when it occurred denied having such knowledge,” the report said. The teacher’s personnel file contained “no evidence of inappropriate conduct with students,” the report said.

The teacher, reached by phone, denied the allegations and referred questions to KIPP.

Debevoise found that the student told an unnamed staff member about the inappropriate behavior in 2014 and that person had not passed the information along to the network. On Tuesday, KIPP fired Mr. Martinez, saying that he was the staff member and that he should have taken action.

Mr. Martinez did not return a call requesting comment after he had been fired.

When asked why she declined to speak to the investigators, the former student said, “I knew they weren’t going to have my best interest at heart. The students, we said to each other, ‘Don’t speak to them. They’re not for us.’”

In the second case, a woman identified as Student 2, who also graduated from the middle school in the early 2000s, said that another teacher had abused her. She, too, did not speak to the investigators, and they were unable to reach a conclusion about whether misconduct had taken place. However, the report noted that the teacher involved had quickly been fired after the school was told he had kissed another student and exchanged inappropriate text messages with her. He was later arrested.

Patrice O’Shaughnessy, a spokeswoman for the Bronx district attorney’s office, said in an email that the office was investigating allegations involving two former KIPP teachers and encouraged anyone with information to contact the child abuse and sex crimes bureau.