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Israeli officials convened an emergency security cabinet meeting amid the new details in the search for the three teens with Israeli Prime Minister Benjamin Netanyahu giving a statement beforehand.
"Hamas is responsible. Hamas will pay," he said, adding that the three teenagers "were kidnapped and murdered in cold blood by wild beasts".
US President Barack Obama criticised the deaths as a "senseless act of terror against innocent youth" while British Prime Minister David Cameron said their deaths were the result of an "appalling and inexcusable act of terror".
The group, which runs the Gaza Strip, has denied any involvement in the kidnapping and killing of the teenagers.
Israeli Defence Forces (IDF) sent in troops in the Hebron area and set up roadblocks around the city, following the new developments in the investigation.
Clashes with Palestinian protesters erupted in the city of Halhoul, north of Hebron, and IDF troops adopted crowd dispersal measures, Ynet newspaper reported.
Some IDF vehicles were reported damaged during the clashes. Twitter user Zishey Twersky wrote:
The youths disappeared while hitchhiking home at night from the Jewish settlement of Gush Etzion.
Israel launched a wide-range operation in the West Bank to find them. More than 400 people, most said to be members of Hamas, were arrested and more than 1,300 sites were searched.
The massive manhunt exacerbated tension in the region and six Palestinians have been so far killed in clashes with Israeli forces.
Israel's internal security agency Shin Bet named Marwan Qawasmeh and Amer Abu Aisha as suspects last week, saying the two were associated with Hamas and had served time in an Israeli prison for "terrorist activity".
"The two principal terrorist suspects in the kidnapping are Marwan Kawasmeh and Amer Abu Eisheh, members of Hamas in Hebron, who are wanted" by Israeli authorities, said a Shin Bet statement.