More than 100 others, including 54 police officers, were injured in the two protests on Friday, both of which turned violent when the students began throwing stones and attacking officers sent to keep watch over them, said the home minister of Meghalaya state, Mukul Sangma.
"Hundreds of students marching in two district towns in protest against a government decision turned violent and attacked policemen and magistrates on duty with stones and other missiles, forcing the police to open fire," he said.
Following the protests in Tura and William Nagar, the authorities imposed curfews in the towns, both of which are dominated by people from the Garo tribe, Sangma said.
The demonstrations were held to protest a government decision to move the Meghalaya State Education Board from Tura to Shillong, a city dominated by the Khasi tribe, he added.
The education board oversees the school syllabus and conducts the examinations in Meghalaya, a remote state of less than two million people.
"The police would obviously not have fired unless the situation turned critical"
Meghalaya state home minister
Five protesters died at the scene of the shootings in Tura while four others were killed in nearby William Nagar, Sangma said.
Another three students succumbed to injuries at hospitals in the two towns, located around 200km west of Gauhati, the capital of the adjoining Assam state and one of northeastern India's major cities.
"The police would obviously not have fired unless the situation turned critical," Sangma said.
He also the authorities had ordered an investigation into the incident.