The two officers were on patrol around their base in the Jordan Valley when they were "misidentified and mistakenly killed" by Israeli army fire, the military said on Twitter.
"Immense sorrow this morning with the announcement of the death of two officers of Unit Egoz," said Defence Minister Benny Gantz, adding that an in-depth investigation was already under way.
Egoz is an elite commando unit of the Israeli army specialised in counterinsurgency.
Prime Minister Naftali Bennett sent condolences "in the name of the whole Israeli people" and promised the necessary lessons would be learnt.
According to investigators, the officers left their quarters and headed to a training area at around 11:00 pm (2100 GMT), probably to go out on patrol.
Shortly afterwards, they identified what they thought was a suspect and fired warning shots in the air.
A soldier from the same unit, who was apparently on patrol nearby, fired at the officers, not realising they were soldiers and believing that he was under fire, and killed two of them.
Last week, two Israeli air force pilots were killed when their helicopter crashed into the Mediterranean off the port city of Haifa following a technical fault.
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