Police today apprehended two classmates of the deceased who were absent since the incident and booked them for murder, a police official said.
As per preliminary investigation, the accused duo had objected to the student for staring at a girl in his class and attacked him with a sickle, he said.
According to the official, the duo--one of them juvenile and another a 20-year-old--allegedly attacked the 16-year-old near the computer room of the school in Pirale village ahead of practical tests for class 10.
"The 16-year-old was attacked with a sickle near the computer room of the school. He was rushed to a hospital by school authorities where he was declared brought dead," the official said.
Natepute police station in-charge Rajkumar Bhujbal said they suspected the role of the two students as they were missing since the day of the incident and even didn't appear for the practical examination.
"An offence of murder was registered against the duo who were apprehended from the village this morning," Mr Bhujbal said.
The officer said a scuffle had broken out between the duo and the 16-year-old after they accused him of staring at a girl in the class, before the fatal attack.
Further investigation is underway, he added.