The police said the SUV of Deputy Speaker Sanbor Shullai was set on fire by the agitators at Jaiaw here at about noon today.
Shullai was not in the car but the driver and his personal security officer managed to flee, the sources said.
Many shops were ransacked and some non-indigenous residents were beaten up in Burabazar in the city last night while petrol bombs were lobbed at Garikhana and Laitumkhrah while a hay stack was set on fire at Nongmynsong, the said.
The NGO activists had also burnt two vehicles -- a government vehicle and a truck -- in the city yesterday.
The first vehicle was torched within minutes of a rally convened by four prominent NGOs ended in the capital.
The four NGOs were Khasi Students Union, the Federation of Khasi Jaintia and Garo People, the Synjuk Seng Samla Shnong and the Hynniewtrep National Youth Front.
Security in and around the city, particularly vulnerable areas, were tightened in view of the agitation of the NGOs, Director General of Police N Ramachandran told PTI.
Ramachandran had met Governor R S Mooshahary last night and briefed him about the law and order situation in the state and in the city in particular, Raj Bhavan sources said. MORE PTI JOP NN