A longtime special education teacher at St. Paul's Humboldt Junior High School is being investigated by police after a 14-year-old special education student said the teacher sexually assaulted her and told her not to tell anybody about it.

According to a search warrant filed Thursday, police searched the suspect's house on Oct. 1, looking for child pornography. They removed a laptop, two hard drives and a plastic bag with pictures in it.

No charges have been filed, and the teacher is not in custody. Pending further investigation, the teacher has been on paid administrative leave since Sept. 25, soon after the girl's mother first raised concerns about him.

Police spokesman Peter Panos confirmed Thursday that the search warrant was served and said that "at this point, there was no evidence gathered that would substantiate the allegations."

According to the warrant:

The girl had transferred from Humboldt Junior High School to Battle Creek Middle School before the 2008-09 school year because her mother thought she was stressed at Humboldt.

On Sept. 19, the teacher left Humboldt abruptly one day, saying he had a doctor's appointment, and went to visit the girl's classroom at Battle Creek, while also visiting another colleague in the building.

He spoke to her outside of the classroom and "told her that she looked nice because she had lost weight and looked pretty in her skirt."

The mother told police that she had become suspicious of the teacher's visits with her daughter and that twice over the last year the teacher called the girl's home and left messages asking about her welfare. The mother also noticed behavioral changes in her daughter.

He showed her pictures

While the district was investigating, the girl told a school social worker that while she attended Humboldt, the teacher would "hit her breast area" when he leaned over her from behind and had shown her pictures of himself as a young adult wearing only underwear.

During an interview with the Midwest Children's Resource Center on Sept. 29, the girl said the teacher had once "put her on his desk and sexually assaulted her in his classroom," having sex with her. Once he was finished, the search warrant alleges, "he told her not to tell anybody and to go back to class."

The St. Paul school district sent a letter home with Humboldt students Thursday saying that an unnamed teacher has been placed on paid administrative leave pending "an investigation into this employee's conduct."

Commander Shari Gray, who heads the St. Paul police sex-crimes unit, said the case was being presented to the Ramsey County Attorney's Office for consideration of charges. She added that the teacher "was very cooperative with the investigation."

Police also searched two classrooms at Humboldt, as well as the district's central administration building. The district is also conducting its own investigation into the teacher, who has also coached various high school sports in the district, including baseball.

The teacher did not return a phone call seeking comment Thursday.

"We're working with the family to provide the girl with whatever she needs" in terms of district or outside resources, said Denise Quinlan, executive director of the middle grades for the school district. " ... School should be the safest place in the world for kids to go to."

Anthony Lonetree contributed to this report. Emily Johns • 651-298-1541