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"They were kidnapped and murdered in cold blood by beasts," Prime Minister Benjamin Netanyahu said in a statement after the military discovered on Monday the remains of the Jewish seminary students who disappeared on June 12.
"Hamas is responsible and Hamas will pay," he said.
U.S. President Barack Obama condemned the killings but called on all parties to exercise restraint.
Netanyahu, who earlier on Monday held Hamas responsible for new rocket strikes from Gaza, convened his security cabinet to consider moves against the Islamist group, which has neither confirmed nor denied Israel's allegations about the kidnapping.
The senior ministers ended their late-night session without taking any final decisions and plan to reconvene later on Tuesday, a government official said.
"Netanyahu's threats against Gaza and against Hamas do not frighten us," the movement's Gaza-based leader, Ismail Haniyeh, was quoted as saying by its Al-Quds television station.
At the square in Tel Aviv where Israeli Prime Minister Yitzhak Rabin was assassinated in 1995, scores of Israelis lit memorial candles for the teenagers, a day after thousands attended a prayer vigil for them at the same spot.
Hamas has been rocked by the arrest of dozens of its activists in an Israeli military sweep in the West Bank over the past three weeks during a search for the teenagers that Israel said was also aimed at weakening the militant movement
Up to six Palestinians died as a result of the Israeli operation, local residents said.
"On behalf of the people of Israel, I wish to tell their dear families ... our hearts are bleeding, the entire nation is weeping with you," Netanyahu said in the statement.
The bodies of Gil-Ad Shaer and U.S.-Israeli national Naftali Fraenkel, both 16, and Eyal Yifrah, 19, were found in a field near Hebron, a militant stronghold, not far from a road where they were believed to have been abducted while hitchhiking, security officials said.
The teens, who attended a religious school in a Jewish settlement, had apparently been shot soon after having been taken, the officials said. Two of the youths lived in Israel.
"They were under a pile of rocks, in an open field," said Lieutenant-Colonel Peter Lerner, a military spokesman.
The alleged abductors are still at large. Israeli media said the break in the case came after their relatives were interrogated.
Troops set off explosions in the family homes of the alleged abductors, blowing open a doorway in one, an army spokeswoman said, while television footage showed the other on fire after the blast. Neighbours said both houses were empty.
After news of the teenagers' deaths, condolence messages and condemnation of the killings poured in from foreign leaders.
"The United States condemns in the strongest possible terms, this senseless act of terror against innocent youths," Obama said in a statement. "I also urge all parties to refrain from steps that could further destabilise the situation."
Netanyahu seized on the abduction to demand Western-backed Palestinian President Mahmoud Abbas abrogate a reconciliation deal he reached with Hamas, his long-time rival, in April that led to a unity Palestinian government on June 2.
Abbas condemned the abduction and pledged the cooperation of his security forces, drawing criticism from Hamas and undercutting his popularity among Palestinians angered by what they saw as his collusion with Israel.
Hamas, which has maintained security control of the Gaza Strip since the unity deal, is shunned by the West over its refusal to renounce violence. The group has called for Israel's destruction, although various officials have at times indicated a willingness to negotiate a long-term ceasefire.