Israel's military says its soldiers have exchanged gunfire with Palestinians during raids in the West Bank in the hunt for three missing teenagers.
It said Israeli troops used live ammunition after being attacked by some 300 Palestinians in Jenin overnight.
Clashes erupted after 30 Palestinians were arrested in the investigation over the missing Jewish seminary students.
The total number of Palestinians detained in the search is now 280.
Israel says 200 of these were "operatives" of Hamas, who Israeli Prime Minister Benjamin Netanyahu has accused of abducting the students.
Hamas has dismissed the allegation that it is involved as "stupid".
No group has claimed to have taken the students, who disappeared last Thursday.
In a statement, the Israeli military said 300 Palestinians, including some who "hurled explosives and opened fire", confronted soldiers who entered Jenin looking for the three seminary students.
"The soldiers responded with live fire, identifying hits," it said.
Clashes also broke out in Nablus, prompting several arrests, the army added.
Palestinian medical sources said at least three people were wounded in the violence. There were no reported Israeli casualties.
Naftali Frenkel and Gilad Shaar, who are both 16, and 19-year-old Eyal Yifrach went missing at a junction near the city of Hebron as they hitchhiked their way home.
Naftali Frenkel holds US-Israeli citizenship.
The military said that troops had searched some 100 locations and raided institutions it said were used by Hamas.
"Militant operatives are paying a heavy price for the abduction of Eyal, Gilad and Naftali," Israeli Lt Col Peter Lerner was quoted in the statement as saying.
Palestinian Authority President Mahmoud Abbas, in a statement, has criticised Israel for using the teenagers' disappearance "a pretext to impose tough punishment against our people and besiege them" in violation of international humanitarian law.
Mr Abbas said on Wednesday that the Palestinian Authority was co-ordinating efforts with Israel in the search, comments that drew sharp condemnation from Hamas, which said the remarks were "unjustified" and "harmful" to the Palestinian reconciliation deal between it and Mr Abbas's Fatah faction.
A unity government supported by Hamas was formed this month, replacing the rival administrations in the West Bank and Gaza.
On Wednesday, Israel detained 65 Palestinians over the students' disappearance, including 51 who were freed as part of a prisoner swap in 2011 in return for Israeli solider Sgt Gilad Shalit.