The man said he was herding his flock of around 70 sheep near the Nablus-area village of Einabus when several Israeli men came from the direction of the Yitzhar settlement.
He said they attacked him and slaughtered five of his sheep, while a number of the animals ran away.
He told investigators from the Israeli human rights organization Yesh Din that his head and arm were injured in the attack and that he was treated for his injuries at a Nablus hospital.
The office of the Israel Defense Forces spokesman confirmed that it had received a report and that the information was passed on to the police.
Photographs from the scene showed the bodies of five sheep, which had been slit from the throat to the chest.
Yitzhar and the surrounding area has been a regular flash point for confrontations between Israelis and Palestinians.
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In recent weeks, a number of incidents of stone throwing have been reported, including one this month in which Israelis allegedly threw stones at the nearby village of Burin.
Last month there was a report that Israelis had vandalized Palestinian-owned olive trees in the area, near the village of Huwara.
Jewish settlers in the area, meanwhile, have reported on a weekly basis that they have been the targets of stone-throwing near Palestinian communities in the area.