It was the first time that charges have been pressed over acts of vandalism by Jewish extremists which were not directly related to government demolition of rogue settler outposts, local media said.
The three, from the Havat Gilad settler outpost in the northern West Bank, were reportedly the first to be interrogated by the Shin Bet internal security service under the provisions of a 2013 defence ministry directive defining perpetrators of price tag attacks as "members of an illegal organisation."
"Price tag" is the euphemism for hate crimes that generally target Arabs.
Initially carried out against Palestinians in retaliation for state moves to dismantle unauthorised settler outposts, the attacks have become a much broader phenomenon targeting anyone seen as hostile to the settlers.
Perpetrators of the attacks have also targeted Muslim and Christian sites, as well as Arab property in Israel.
According to the charge sheet, the three men- aged 22, 23 and 35- set fire to two vehicles and spray-painted stars of David on village walls in their November rampage.