"The FIR filed in an Ahmedabad police station is a most vindictive act by the (Narendra) Modi government designed as a form of punishment for her fight for justice on behalf of Zakia Jaffri and other victim families of the Gujarat violence in 2002," the party said in a statement.
The CPI-M demands that the FIR be withdrawn.
"It is a measure of the contempt for minimum democratic norms by the Modi government that it has time and again sought to suppress through threats, warnings, false FIRs and concocted stories all efforts by Setalvad and others to bring out the truth behind the role of the chief minister in the violence," it said.
"The timing (of the FIR) is also suspect as Zakia Jaffri is in the process of filing an appeal against the ruling of the lower court in favour of the SIT's clean chit to Modi.
"The latest effort is condemnable," the Communist Party of India-Marxist said. "The CPI-M demands that the FIR be withdrawn."