"The inquiry will probe the matter of kidnapping of three youths -- Kundan Basumatary, Rajib Basumatary and Rajkumar Rabha -- on December 21," an official statement said.
The three, all from Narayanpur village in Baksa district, were picked up from Narayanpur Bazar by a group of men wearing Army uniform.
The body of Rajib was found at Dalongpar under Tamulpur Police station on December 23.
Rajkumar escaped with multiple wounds and claimed that their kidnappers had asked them about illegal weapons, tortured them and killed Rajib.
The third youth, Kundan, remains untraced so far, police said.
The kidnapping and killing has spread outrage across the Bodoland Territorial Area Districts (BTAD) region with many alleging involvement of the Army in the incident.
"The magisterial inquiry will look into the whole matter of kidnapping and murder and the report will be submitted soon," the statement said.
Meanwhile in another statement, the Army denied any involvement in the incident and said it had also ordered an investigation into the matter.