Pema Khandu has also announced an ex-gratia for the next of the families of the dead.
Arunachal Pradesh Chief Minister Pema Khandu said on Monday certain "forces" were behind the violent protests in the state over the granting of permanent residency to six non-native communities.
In a statement, Mr Khandu appealed to the people to end the protests and cooperate with the government in maintaining peace, saying the administration had already cleared its stand on the permanent residence certificate (PRC).
"I believe that there are forces behind these incidents as Arunachal is a peaceful state, particularly Itanagar," Mr Khandu said.
Stating that the issue "is closed", the chief minister hinted at a communication gap for which the latest government stand on the PRC had not reached the people and led to violence.
Mr Khandu said a commissioner-level inquiry had been ordered into the incidents and damage caused by the protests. He announced an ex-gratia for the next of the families of the dead.
The chief minister also talked over phone to leaders of various communities who were protesting the PRC issue.
Protests broke out in Itanagar and Naharlagun town on Saturday after the ruling BJP government announced that it was considering issuing PRC to six communities who are not natives of Arunachal Pradesh, but are living in the state for decades. The six communities are Deoris, Sonowal Kacharis, Morans, Gorkhas, Adivasis and Mishings.
The violence have left three people dead, including two in police firing, as mobs rampaged through the streets clashing with security forces, setting on fire hundreds of buses and damaging public and private properties.