Police said the jawans were injured when their convoy was attacked near Umiam on the outskirts of the capital city on the second day of the Khasi Students Union (KSU)-sponsored three-day night road blockade.
Four jawans were admitted to the Shillong Civil Hospital. Another injured jawan was released after first aid.
Police said an office of the state horticulture department was set ablaze in West Khasi Hills district.
Two government vehicles were torched by petrol bombs in two different localities of Shillong. A private taxi was also torched in the city. A truck was set afire near Nongpoh in Ri Bhoi district.