The charges concern orders given that led to the violent dispersal of protesters trying to disrupt a military parade, and the "fraudulent" seizure of the Imedi TV station in 2009.
Also charged were ex-interior minister Vano Merabishvili, former justice minister Zurab Adeishvili, ex-defence minister David Kezarashvili and the former mayor of the capital Tbilisi, Gigi Ugulava.
Saakashvili, who is in self-imposed exile in the United States, did not return to Tbilisi for questioning by prosecutors.
Saakashvili refused several months ago to return to Georgia to testify as a witness in several criminal cases, saying he did not have confidence in the country's current rulers.
A staunch US ally and flamboyant reformer, Saakashvili ruled Georgia for a decade until his party lost parliamentary elections in 2012.
Since then, a number of Saakashvili's top allies have been investigated and some jailed, prompting Western concerns over politically motivated trials.