Hillary Okeyo was charged on Wednesday with two counts of defiling and committing indecent act to the 15 year old student.
The Biology teacher at Highridge Secondary School in Nairobi denied all the charges before Nairobi Chief Magistrate Daniel Ogembo and was remanded in police custody until Friday when his bail application will be determined.
The prosecution was opposed to his release, saying he is likely to interfere with evidence by contacting students and staff who are listed to testify against him.
Meanwhile the School management is alleged to have protected the teacher, while risking the life of the student, who was reportedly abused last Wednesday.
The institution has also been accused of inaction for two days and only took the girl to hospital on Saturday after her colleagues refused to go to class over the issue.