The accusations have prompted increase scrutiny of the officers, known as carabineros, by students and the international press, The Santiago Times reported.
Director of Security and Public Order Alfonso Munoz, who oversees the carabineros, announced the probe after meeting with three of the 10 students accusing the police and a senator.
Munoz did not disclose the names or ranks of those officers who will be investigated.
The lack of disclosure angered at least one of the students.
"The names must be made public; the people need to know the carabineros we have," said Ignacio Munoz.
The students, seven males and three females, said they were part of a student occupation of a school about 50 miles south of Santiago when members of the police unit arrived and forced the students out of the building.
The students were taken to the police station, where they said police ordered them to strip naked.
In a separate incident Thursday, carabineros breaking up a student strike were accused of sexually assaulting protesters.
A report by The New York Times during the weekend said that "acts of sexual humiliation" by the uniformed police were becoming more frequent.