An assistant principal at a high school in New Haven is accused of sexually assaulting a female student.

Daniel Bonet, 49, was arrested by the New Haven Police Department on Monday and charged with second-degree sexual assault and fourth-degree sexual assault, according to court records. Both charges were filed under a provision dealing with someone who was in a supervisory position over the victim, court records show.

According to the arrest warrant affidavit, police launched an investigation on May 22 when they received a report from the Connecticut Department of Children and Families. The agency learned through a Hillhouse High School employee that a student reported an incident in which she alleged her and Bonet were alone in his office with the door closed, the warrant affidavit said.

The girl first disclosed the allegations to a former school official the same day they happened. She referred to her as her “school mom,” the official told police, according to the warrant affidavit.

The girl also provided a social worker at the school additional details about the incident in a series of text messages in which she alleged that Bonet grabbed her arm and pulled her in for a kiss, the warrant affidavit said. The girl said she did not know what to do so she allowed the kiss to happen, describing it as a “tongue kiss.”

According to the warrant affidavit, the girl alleged that Bonet sat her on his desk, unzipped her shirt and pulled down her pants before touching her inappropriately in multiple places. She alleged that he kissed her neck, stomach and multiple other parts of her body, the warrant affidavit said.

The girl said the incident only ended when Bonet was contacted through his school radio, police wrote. She said she went to the bathroom afterward where she was crying and shaking.

“And now that’s all that’s playing in my head,” the girl wrote in a text message.

The girl also alleged to school officials that Bonet had kissed on a previous occasion a day earlier, the warrant affidavit said.

After reporting the allegations, the girl was taken Yale New Haven Hospital where a sexual assault kit was performed.

During a forensic interview, the girl gave investigators additional details about the allegations, including those involving the first incident. During the first encounter, the girl said Bonet allegedly kissed her after giving her a hug to console her, as she was crying about “things at home” while the two were alone together in his office, the warrant affidavit said. She also alleged that one of her friends called her while it was happening and that she tried to pick up, but that Bonet took the phone and moved it, police wrote.

The girl said her friend later knocked on the office door during the incident and questioned why it took her so long for someone to open it, the warrant affidavit said.

The following day, the girl said Bonet had her come to his office, the warrant affidavit said. When another student arrived, the girl claimed that he instructed her to leave, police wrote.

The girl described the accusations in great detail for investigators. Afterward, she said, she went to a bathroom to change her clothes because she felt dirty, the warrant affidavit said.

Through the school’s surveillance system, police said they were able to confirm that Bonet was alone in his office with the girl on the two days when she said the allegations happened, according to the warrant affidavit. During the second incident, police said the surveillance allegedly showed that the two were alone together for a little over an hour and that no one answered the door when someone approached the office and knocked, the warrant affidavit said.

When police spoke to the former school official who first learned of the allegations, she told investigators that she was uncomfortable at times with the relationship between Bonet and the girl, as the two would reportedly hug often, the warrant affidavit said. She said their interactions sometimes would not “sit well” with her and made her feel “icky,” as Bonet would pick the student up to give her a hug, police wrote.

A social worker at the school also spoke with police and said the student would “constantly” come to her office throughout the school day for therapeutic services, the warrant affidavit said. She said the girl often became attached to adults because of past trauma and that she would refer to Bonet as her “school dad,” police wrote.

When authorities tried to interview Bonet, he told them he was “not refusing” to speak but that he was advised to have investigators reach out to his attorney, the warrant affidavit said.

Police later obtained a search warrant allowing them to collect a DNA sample from Bonet. They compared the DNA to multiple samples taken from the victim during the sexual assault kit.

According to the warrant, Bonet could not be eliminated as a contributor from one of the samples and was believed to be a likely contributor to a second sample. Multiple other samples that were examined showed inconclusive results.

“It’s too early in the case to really comment,” Bonet’s attorney, New Haven-based lawyer Don Cretella said, Wednesday. “We’re reviewing all the discovery and beginning our defense. Other than that there’s not really much to say at this point.”

Bonet is free on a $250,000 bond and is scheduled to appear in New Haven Superior Court on Oct. 8.

New Haven city officials last week said Bonet was placed on administrative leave once school officials learned of the accusations. According to the warrant affidavit, however, a school official told police she saw Bonet working at the school as late as May 26, four days after police and DCF began investigating.

A spokesperson for the New Haven Public Schools said Wednesday that, after the student reported the accusations, Bonet was “placed on leave the next school day in accordance with NHPS protocols.”

An interim replacement is expected to fill the vacant position.

“We are working with our school social workers and specialized staff to support our students and staff,” the school district spokesperson said, adding that officials are committed to “maintaining a healthy and supportive school community.”

“Support is available for any students and staff who need it,” the spokesperson said. “Nothing is more important than the safety of our students. Hillhouse families with questions or concerns have been invited to reach out to the school.”