Duangtip Kantapeng was arrested on Saturday on suspicion of having raped the Prathom 5 pupil over a period of almost a year.
Relatives said that on Friday she complained of severe pain and said she had been assaulted. She told them she had been raped at least 10 times at the school since May 2013, the most recent was on Friday, and that her attacker threatened to kill her if she told anyone.
Her family was determined to find out what had happened and filed a police conmplaint.
The school janitor was arrested on Saturday and was scheduled to appear in court Monday when police would seek to extend his detention in custody.
Protesting villagers said if the man was released on bail they would stop sending their children to the school.
Songpilas Wongway, a social development and human security official, later told the villagers the police would detain the man for a further 12 days without bail, and the case would then follow legal procedure.
Pol Lt Pol Prakorb Kamdee, a case investigator at Mae Jai police station, said the suspect still denied the charge so the police would have to question the girl further and find evidence to strengthen the case against him.