These properties reportedly belong to trusts run by Haryana minister Captain Abhimanyu, CBI sources said.
The CBI move comes after the Centre referred the cases to it on February 6, 2017, nearly an year after the incidents.
At least 30 people were killed and properties worth crores of rupees were destroyed in Haryana during the violent quota agitation by Jats in February, 2016.
The protesters were seeking reservation in government jobs and educational institutes for the Jat community under the category of Other Backward Classes.
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On February 20, a mob of 100-150 people armed with oil cannisters and rods gathered around the school. They allegedly ransacked the property and put the building, school buses and other vehicles on the properties on fire.
In the complaint, the guard has named several individuals including some former village heads of the area.
CBI has registered a case of rioting and arson against 10 persons on the basis of his statement.
Second FIR pertains to alleged arson at Haribhoomi Press in Rohtak which was also set on fire by a mob in the intervening night of February 19-20.
It is alleged that a loss of around Rs 15.50 crore was caused by the alleged rioters.