In a statement, General Kayani said a military board headed by a Major General would conduct the investigation to determine the authenticity of the five-and-a-half minute video.
Emphasising that Rules of Engagement are sacrosanct, the army chief said such violations of army rules against extra-judicial killings, if true, would not be tolerated.
The video shows the young men blindfolded and being lined up against a wall. Gunfire is then heard, the men crumple and a soldier moves in to shoot each body at short range.
The video, yet to be verified, appears to have been taken in the Swat Valley.
Earlier this week, the United States urged Pakistan to investigate the video clips on the internet that appear to show Pakistani soldiers summarily executing six blindfolded young men.
Pakistan Army has dismissed allegations of extra-judicial killings and termed the videos claiming to show soldiers gunning down blindfolded men as fake.
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