A statement from the archdiocese of New York last week on the day a teacher at Cathedral High School in Manhattan was arrested said that administrators at the school called the Queens district attorney’s office within an hour of hearing the complaints of two students.

The biology teacher, Richard Ali, 27, was charged with statutory rape, sexual abuse, and endangering the welfare of a child, according to a copy of the criminal complaint from the Queens District Attorney. Mr. Ali was later released on $40,000 bail.

Mr. Ali no longer works at the school, according to a spokesman for the Archdiocese of New York, Joseph Zwilling.

This week, Mr. Zwilling acknowledged that a student and her mother came forward more than two years ago with what they said was an instant-message transcript between the teacher and another student. Five former students told The New York Sun that two years ago, administrators at the school told them that the transcript was inauthentic. A spokesman from the Queens district attorney’s office, Kevin Ryan, said the prosecutor on the case received the transcript from the school on Tuesday morning and that the office has widened its investigation of Mr. Ali.

The 1,916-word transcript includes one person, referred to as “Mr. Ali,” telling the student that “they did a study on how sex keep you healthy when you’re older” and that he finds short skirts with knee-high socks “sexy.” The person alleged to be Mr. Ali proposes that he go to the student’s house when her parents aren’t home to engage in sexual activity. The conversation takes places between about 5:08 p.m. and 5:40 p.m., according to a time log on the transcript.

Mr. Zwilling said administrators had questioned both Mr. Ali and the student about the transcript after the allegation was made, but both denied they were involved. The school’s technology coordinator checked Mr. Ali’s computer at the school and “found nothing inappropriate,” Mr. Zwilling said.

The transcript emerged while a separate “cyber-bullying case” was going on, he said.

The student who first came forward with suspicions about Mr. Ali, Amanda Castro, 18, a recent graduate of the school, said a mutual friend sent her the transcript and that she and her mother approached the vice principal of student life, Elizabeth Lawlor, with it in January 2005. Ms. Castro said Ms. Lawlor accused her of falsifying the transcript to get back at the other girl, whom the New York Sun is not identifying.

“They didn’t believe me because I didn’t like the girl,” Ms. Castro said, later adding: “I’m upset. This could have been prevented.”

Ms. Lawlor did not return calls or e-mails from the Sun.

Cathedral High School is located in Midtown, at 350 E. 56th Street, but the crimes Mr. Ali is charged with took place in Queens, according to the criminal complaint. He allegedly had sex with a female under the age of 17 in a car while it was parked in the vicinity of Long Island City High School in January.

During the 2006-07 school year, Mr. Ali also called another student, also under the age of 17, multiple times and “spoke about wanting to have sex with the student,” the complaint says. On February 3, he took the student to the Whitestone Movie Cinemas, where he rubbed her legs and stomach and touched her breasts, the complaint says.

Mr. Ali’s lawyer at the arraignment, Scott Dufault, declined to comment for this article. Messages left at Mr. Ali’s home in the Richmond Hill section of Queens were not returned.

Another recent graduate of Cathedral High School, Alyssa McKay, 18, said Mr. Ali was known to give students rides home and to take them on one-on-one trips to movie theaters and his house.

“They didn’t want that to be true,” she said of school administrators. “He was an honors teacher.”

Amanda Ponte, 18, who is now a freshman at John Jay College of Criminal Justice, said Mr. Ali paid special attention to the students that were in the extra-curricular biology club, which took place after school. He was known for leaning close to students’ faces and staring at their legs, she said.

Still, students didn’t feel comfortable coming forward about his behavior, she said.

“It’s not a school where you can approach somebody, ‘I’m having a problem,'” Ms. Ponte said. “We told the younger students, ‘Be careful. Don’t ever be in a room alone with him, not even the elevator.'”

Mr. Zwilling, the spokesman for the Archdiocese of New York, denied the school’s atmosphere prevented students from coming forward.

“Cathedral Girls High School takes any allegation of sexual misconduct seriously, as evidenced by the prompt contacting of the district attorney’s office last week when a student made an allegation of misbehavior against a teacher,” he said. “No student has ever been suspended or disciplined for bringing forward allegations of misconduct.”

A police source said last week’s call was the first time the New York Police Department was notified about an allegation against Mr. Ali. The source said detectives seized Mr. Ali’s computer from his home, where he lives with his parents, and were combing through it for evidence.

Tuition at the all-girls school is $5,675 a year, and 96% of graduates are accepted to four-year colleges.

Mr. Ali has a court appearance scheduled for April 9, at which time he will have a chance to enter a plea.