"In order to establish the truth behind the Kishtwar violence and what followed, the State Government has decided to order a Judicial inquiry," Omar wrote on micro-blogging site twitter.Com.
The Chief Minister said the inquiry will be held by a retired judge of the High Court and its outcome will be made public.
"The inquiry will be held by a retired High Court judge in a time-bound manner to establish the facts and share them publicly," he said.
Communal clashes broke out in Kishtwar area of Jammu province on Eid day which later spread to other parts of the region including Jammu city and Rajouri town.
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Earlier, the state government had ordered an inquiry by the Divisional Commissioner in to the incident and promised severe punishment to those found responsible for death and destruction in Kishtwar.