The fresh violence around the central West Bank village of Kafr Malik came after the Palestinian health ministry said three men died there in an attack by Israeli settlers on Wednesday.
Soldiers went to disperse a gathering of Israelis near the village overnight, the military said in a statement.
"Dozens of Israeli civilians hurled stones toward them and physically and verbally assaulted the soldiers, including the battalion commander," it said.
"In addition, the civilians vandalised and damaged security forces' vehicles, and attempted to ram the security forces," it added.
"The security forces dispersed the gathering, and six Israeli civilians were apprehended and transferred to the Israel Police for further processing."
Contacted by AFP, the Israeli military declined to say whether those arrested were residents of Israeli settlements in the territory, occupied by Israel since 1967.
The military referred the query to the Israeli police, which was not available to comment.
Prime Minister Benjamin Netanyahu "firmly" condemned the violence in a statement, demanding an "in-depth investigation".
"Anyone who broke the law or acted against our soldiers must be prosecuted with the utmost severity," he added.
- West Bank violence -
On Wednesday the Palestinian health ministry said three men died in Kafr Malik in an attack by settlers.
AFP journalists saw several hundred people gather for the three men's funerals on Thursday.
The Palestinian foreign ministry alleged "official complicity" by Israel in Wednesday's attack, in a message on X.
"Israeli occupation forces prevented ambulance crews from reaching the wounded and obstructed civil defence teams from entering the village for several hours, allowing fires ignited by the settlers to spread and destroy dozens of homes," it said.
The Israeli military did not respond to a request by AFP to comment on those claims.
A military spokesman told AFP its forces intervened on Wednesday after "dozens of Israeli civilians set fire to property in Kafr Malik" and a "confrontation" involving "mutual rock-hurling" broke out between Israelis and Palestinians.
Referring to action by the Palestinians, the spokesman said: "Several terrorists fired from within Kafr Malik and hurled rocks at the forces, who opened fire toward the source of fire and the rock-hurlers."
Five Israelis were arrested, the military added.
Left-leaning Israeli newspaper Haaretz reported that the five were released on Thursday. Police did not comment.
Israeli settlements in the West Bank are considered illegal under international law.
Their growth has accelerated since Prime Minister Benjamin Netanyahu returned to office in 2022 in an alliance with far-right parties who wish to annexe the territory outright.
Countries including Britain and France and several human rights groups have condemned settler violence against Palestinians in the West Bank.
Violence has surged in the West Bank since Israel launched its offensive in Gaza in response to the October 7, 2023 attack by Palestinian militant group Hamas on Israel.
The Palestinian Authority says Israeli troops or settlers have killed 945 Palestinians, many of them militants but also scores of civilians, since the start of the Gaza war, according to Palestinian health ministry figures.
Israel says 35 of its soldiers and civilians have been killed in Palestinian attacks or during Israeli military raids since that date.
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