Security have been beefed in the affected areas and 1,200 paramilitary personnel have been dispatched by the Center.
Prohibitory orders have been sanctioned in Sirsa, where the sect is based, and in Fatehbad, Jind and Hisar in Haryana.
Along with patrolling the streets in the market, tight security has been positioned outside the building of the Dera Sacha Sauda.
However, the shopkeepers have been the most affected by the shutdown.
"There is no law, but if you say there is law and authorities are taking actions against these activities, then what is the point of blocking the daily chores of the city?" said Surinder Joshi, a shopkeeper.
"What is the sense in this? Labourers and workers are highly affected by this especially those who are daily-wage earners; their situation has become miserable," added Joshi.
Earlier on Saturday, Feb 27, the Central Bureau of Investigation had booked Gurmeet Ram Rahim Singh for the murder of a Faqir Chand in 1991, who was working as a manager at the sect's mission.
Four trains and around 37 vehicles, including 27 buses were set ablaze by angry Dera Sacha supporters, and property in several places in Punjab and Haryana were vandalised.