A mob attacked the Chokpot police station, injuring six policemen. Three police vehicles and three motorcycles were set ablaze.
Taking advantage of the melee, suspected militants also fired from a church complex towards police personnel who were rushed in to to control the mob.
However, police did not retaliate as there were many children in the church premises.
"Curfew was imposed in Chokpot from 2 p.m. following an attack on a police station over the custodial death of an accused," Additional District Magistrate T.G. Momin told IANS over phone.
Witson Sangma was arrested on charges of supplying explosives to the outlawed Garo National Liberation Army (GNLA). He was Wednesday found dead in police lockup.
Police said the death was due to hypertension, residents alleged "police excesses".
"The situation is tense but under control," district police chief Lakardor Syiem told IANS.
He said six policemen were hit by stones hurled by the mob.
The Meghalaya Peoples Human Rights Council (MPHRC) criticised police over their abysmal record of custodial deaths.
"In Meghalaya, 20 people have died both in police and judicial custody 2001-2013. There is much evidence from various verdicts of the judiciary and the National Human Rights Commission (NHRC) that a majority of these deaths are a direct implication of torture by police in custody which is a clear violation of human rights," MPHRC chairman Dino D.G. Dympep said.