Gadchiroli district collector Shekhar Singh has ordered a magisterial inquiry into the two encounters last month in which 40 Naxals were killed.
The encounters took place on April 22 and 23, in which 34 and 6 Naxals respectively were killed, an official said.
The inquiry has been ordered as per the provision under section 176 of the Criminal Procedure Code (CrPC), Singh told PTI.
"The sub divisional magistrates of Etapalli and Aheri teshils, in which the encounters took place, will conduct the probe, which is a routine process after any encounter, and submit their reports to the administration," another official said.
The probe comes in the backdrop of allegations that security forces killed "innocent villagers" by poisoning their meals.
Civil rights activists had questioned the authenticity of the encounters as not a single jawan was injured in both the encounters.
The CPI (ML) Liberation sought a judicial inquiry while a noted Telugu poet and civil rights activist Varavara Rao demanded a judicial inquiry with either a sitting or a retired Supreme Court judge.