Pro-Palestinian activists released video footage on Sunday showing an Israeli army commander hitting a Danish activist in the face with his F-16 rifle, dpa reported.
The footage was broadcast on Israeli television.
The Israeli military condemned the incident as "severe" and said it would take "appropriate measures" after a thorough investigation.
The incident happened on Saturday, when a group of pro-Palestinian activists cycled on a road through the Jordan Valley in the West Bank to protest Israeli security restrictions on the movement of Palestinians in the area.
The commander, a lieutenant-colonel, arrived at the scene after receiving a report that activists were blocking the road.
When one of the activists came near him, the commander lifted his F-16 rifle and hit him with it in face, the footage shows.
The Danish national was take to hospital needing stitches to his lip, one activist said.