STORY: Protesters burned passenger trains and buses this week to express their outrage against the new policy.
Heavy police presence was seen around railway stations and hotspot areas where angry protesters caused damage to public property.
Authorities suspended internet services in several parts of eastern state of Bihar in a bid to stop public gatherings and violent protests.
"Resorting to violence and arson is not the solution for any problem. The solution lies in understanding the situation, understanding the scheme," said Indian Air Force Chief Air Chief Marshal Vivek Ram Chaudhari.
One protestor was also killed in police firing in southern Secunderabad city on Friday (17 June) and more than a dozen have been injured in a series of protests, according to local media reports.
The Agnipath or "path of fire" system aims to bring more people into the military on four-year contracts to lower the average age of India's 1.38 million-strong armed forces.