Major Shikhar Thapa was fired upon by a jawan in a fit of rage following an altercation by the soldier on duty at Butcher post in Uri sector, the officials said.
Confirming the killing of the officer by the jawan, a defence spokesman said the Army and police have started investigations into the incident.
"We are ascertaining details," the spokesman said without elaborating further.
Major Thapa rebuked the soldier and warned him about further disciplinary action.
Irked by the reprimand, the soldier fired a few shots from his service rifle at the officer, killing him, the official said, adding, the jawan was overpowered by other jawans and disarmed.
Major Thapa hailed from Dharamshala and is survived by his wife and son.
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