"It will be my humble request to you to constitute high- level special investigation team (SIT) to probe both the FIRs (in Shopian incident). Please give orders to set up a high- level SIT and leave it to them to investigate," Omar said in Assembly.
He was speaking on the grants of home, general administration, planning departments moved by Chief Minister Mehbooba Mufti today.
He said that the magisterial probe, ordered by the state government after incident, would continue separately.
The Army has submitted its version of the January 27 incident, when its convoy was attacked in Shopian district, to the Jammu and Kashmir Police and explained its reasons for opening fire at the stone-pelting mob, officials said today.
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According to the Army's narrative, submitted yesterday, the force's convoy was attacked by a group of stone-pelters and its personnel resorted to firing to save themselves, the officials said.
The FIR filed by the state police does not name any accused but states that a company of 10 Garhwal Rifles led by Major Aditya was on its way for official duty when it was attacked by an unruly mob with stones.
The Shopian incident became a bone of contention between the state's ruling alliance partners PDP and BJP.
A BJP legislator demanded on the floor of the House that the FIR against the Army be cancelled.
Taking a dig at the chief minister, Omar asked why no action had been taken in previous FIRs registered against security forces.
"You have assured the people of the state that FIR will be taken to conclusion. It is good. But till now, there has been no action on FIRs (registered against security forces in the past)," Omar said.
He said that since 2000, the state government had forwarded 50 requests to the Centre to give permission for prosecution of central security forces, particularly the Army, where "we have seen human right violations".
Omar said that the security situation was getting worse in the state.
He batted strongly for the grant of compensation to Farooq Ahmed Dar, who was tied to an Army gypsy and paraded through nine villages on the day of bypoll to the Srinagar Lok Sabha constituency.
"The Army officer who tied him got award but this youth who voted in elections does not deserve even the compensation?" he wondered.
The former chief minister asked Mehbooba Mufti to advise her counterparts in New Delhi not to take decisions for the state from there and to consult the state leadership.