Chesterfield Thangkhiew was allegedly killed in the course of a police raid withinside the state capital, Shillong, on Saturday.
His loss of life sparked mob violence and arson withinside the city, forcing the government to impose a two-day curfew.
Mobile net services had been also suspended in 4 districts.
Officials defined it as an "extreme breakdown of regulation and order".
Thangkhiew, 54, was one of the founding figures of Meghalaya's separatist movement that vies for a separate hometown for its tribal population.
Police say Thangkhiew was killed in "retaliatory firing" all through a raid at his domestic in Shillong. But his own circle of relatives referred to as it "cold-blooded murder" - they allege the police orchestrated a "faux encounter", an Indian term for extrajudicial killings through government.
On Sunday, indignant protesters threw petrol bombs at Chief Minister Conard Sangma's private house in Shillong. However, no one was hurt because the chief minister remains at his official house.
Incidents of stone-pelting had been additionally stated from throughout the city.
The state's Home Minister, Lahkmen Rymbui, referred to as for a judicial inquiry into the problem and stated he was resigning "to carry out the truth".