The functioning of the judicial commission had come to standstill since four months due to the death of Justice Sarat Chandra Mohapatra, who had headed the panel.
The home department had already decided to install Justice Naidu to carry forward the probe and a formal official notification in this regard is expected to be issued soon, sources said.
Saraswati was killed on August 23, 2008 in Kandhamal along with four of his disciples. The entire district witnessed large scale communal violence in which 38 people were
killed besides burning of over 4,000 houses.
The state government had set up a judicial commission headed by Justice Mohapatra to probe the matter from September 17, 2008. The commission has so far received nearly 700 affidavits.
Sixty-five government and 99 private witnesses have so far been examined by the commission. The examination of three witnesses were halfway through when justice Mohapatra passed away on May 12.
The crime branch is investigating the matter and arrested 10 persons and submitted chargesheets against 14 persons in connection with the incident.
