The Southern Command unveiled the flag of size 225 feet by 150 feet at Jaisalmer Military Station.
The police have already registered a case and launched an investigation into the matter by constituting a special squad.
A 1,000 kg handwoven khadi tricolour, the largest in the country, was unfurled atop a high mountain overlooking the Leh valley on Saturday to commemorate Gandhi Jayanti and the 75th anniversary of India's Independence.