The report was handed over to the 15 Corps Commander Lt Gen N C Marwah.
The police, in its preliminary probe, have alleged that Major Opinder and his team members including two subedar majors and a sepoy allegedly entered into a criminal conspiracy with locals of Rafiabad including a jawan of Territorial Army -- Abbas Shah -- and kidnapped three youths on the pretext of providing them job, official sources said.
They were later killed on April 30 after being labelled as terrorists. After receiving the report, Army today ordered a high-level enquiry into the alleged fake encounter and said that proceedings will be "judiciously expedited".
"Based on the preliminary report of the Machhil encounter, received from Jammu and Kashmir Police late evening on 29 May, a high-level enquiry has been ordered by the Army," a defence spokesman said.
He said the enquiry will investigate all allegation, based on the report submitted by the police and efforts were on to "recall" the witnesses as their unit had been de-inducted.
"We will judiciously expedite the proceedings as promised," spokesman Lt Col J S Brar said.
"The only delay we foresee is the recalling of the witnesses who are involved in the incident as the unit has de-inducted after competing its mandated tenure. However, efforts to get them back have already been initiated", he said.
Personnel of 4 Rajputana Rifles had said that they had gunned down the three "militants" while they were attempting to enter into the Valley from across the border on April 30.
However, the claim of the army was contested by the family members of Muhammad Shafi, Shehzad Ahmed and Riyaz Ahmed who said they were not militants.
The police registered a case of missing on April 27 followed by kidnapping and later arrested four persons including Abbas. The other three were Qayyum Shah, Basharat Lone and Abdul Hamid Bhat.
Police will also register a murder case against the Major and some civilians in connection with the case, officials said.
The state government has ordered a magisterial enquiry into the case and also taken up the matter with the Defence Ministry.
Defence Minister A K Antony had yesterday said that the army will cooperate in the probe and the guilty will not be spared.
The bodies of the three men were exhumed on Friday and identified by the relatives. Authorities handed them over for last rites after taking DNA samples. The trio were buried in the local graveyard in Nadihal-Rafiabad, 65 km from here, yesterday.