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A Palestinian teen has been shot dead by Israeli troops who opened fire on protesters as they swept a West Bank town in the search for three missing students.

Israel Defence Forces (IDF) said they conducted night raids in four Palestinian towns and arrested 25 suspects in connection to the alleged kidnapping of three Jewish teenage seminary students reported missing last week.

In Dura, near Hebron, IDF troops were met by stone-throwing Palestinian youths and opened fire. Mohammed Dodeen, 15, was killed by a bullet in the chest, hospital officials said.

Another three Palestinians were seriously wounded by IDF gunfire in separate clashes in the Qalandiya refugee camp.

An official at a hospital in Ramallah said one was in intensive care while the other two were in serious condition.

The IDF maintained soldiers used live fire only in response to life-threatening situations, and claimed Palestinians threw home-made explosives, firebombs, fireworks and stones. In Qalandiya, a soldier was slightly injured by a grenade.

Missing Israeli teenagers Naftali Frenkel, Gilad Shaar and Eyal Yifrach
Missing Israeli teenagers Naftali Frenkel, Gilad Shaar and Eyal Yifrach. IDF

The confrontations erupted as IDF troops searched about 200 locations for 16-year-olds Naftali Frenkel, Gilad Shaar and 19-year-old Eyal Yifrach who disappeared while hitchhiking from a Jewish settlement seven days ago.

Israel says the youths have been kidnapped by Islamic militant group Hamas and a massive manhunt has been launched, involving thousands of troops.

Almost 300 people have been held, including 51 Palestinians who were released by Israel in a prisoner swap deal three years ago.

The crisis has caused an escalation of tension between Israel and the Palestinian Authority.

Palestinian president Mahmoud Abbas has condemned both the abduction and Israel's sweeping response.

Hamas, which has abducted Israelis before, praised the abduction of the teenagers but has not claimed responsibility for it. No demand for ransom has been issued.

Earlier this week, it emerged that Israeli police ignored an emergency call from one of the missing teenagers.

One of the boys called the police hotline shortly after the three disappeared and whispered "I've been kidnapped" before the line went dead. The call was dismissed as a prank by the police operator.