The Joint Action Committees of Kakwa in Imphal West district and Lilong in Thoubal district joined hands with the United Committee Manipur and All Manipur United Clubs Organisation to call the shutdown.
Sagolshem Prasanta was found dead on April 26 at Lilong in Thoubal district. The strike began at midnight on Wednesday.
On Thursday, some activists were caught on camera smashing windscreens of many varieties of vehicles.
They said they decided to go ahead with the strike after Chief Minister Okram Ibobi Singh refused to share with them a copy of the autopsy report.
Fuel stations and markets in the Imphal city were closed down. Passenger and other vehicles went off the roads.
But markets in some remote areas remained open. There was thin attendance in government offices. Educational institutes were closed.