In a statement, the Israeli military said Prime Minister Benjamin Netanyahu had authorised the operation against Al-Atta, blaming him for recent rocket, drone and sniper attacks against Israel, and attempted infiltrations into the country.
"The home of a member of the political bureau of the Islamic Jihad movement in Palestine, Akram Al Ajouri, was also targeted in Damascus, killing one of his sons", it said.
Syria's state-run news agency says Israel has struck a residential building in Damascus housing a commander of the Palestinian Islamic Jihad group with two missiles, killing two people.
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Minutes after the Iranian-backed group confirmed the death of the commander, Bahaa Abu el-Atta, at dawn, barrages of rockets could be heard fired toward southern Israel from Gaza. The house was known to be Abu el-Atta's home.
He said that Hamas would never take an isolated decision in any of the Palestinian issues, and that any measure must be discussed with the other Palestinian factions and a collective decision be taken by all of them together.
Israeli authorities said schools across southern Israel and the Tel Aviv region were closed after rockets reached the area. Al-Ajouri's son Muath was killed, along with his granddaughter Batoul. A separate missile strike reportedly hit a civilian building near the Lebanese Embassy in the western district of the capital that is home to Damascus University and several diplomatic missions.
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"Kahol Lavan will back up any activity that is right for Israel's security and put the safety of the people above politics". Bennett has long advocated tougher action against Palestinian militants, including a resumption of targeted killings. Bennet has been clamouring for a more aggressive stance toward Gaza.
Israel routinely says it holds hold Hamas responsible for any fire emanating from the enclave but acknowledges that the vast majority of attacks are carried out by the smaller and more radical Islamic Jihad group.
The overnight attacks mark a significant escalation in the conflict between Israel and the Palestinian militant groups, which have fought each other in wars and cross-border violence for years.
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Islamic Jihad reports that his wife and children were also killed in the attack.