Hamas is considered a terrorist organisation by Israel, the United States and the European Union.
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Three Hamas training camps and a security complex were targeted in the air strikes and a passerby was hurt, witnesses said.
From past Israeli interceptions the possibility of a violent military attack as was experienced by the Mavi Marmara flotilla in 2010 is a reality.
Ahfad al-Sahaba claimed responsibility for a separate rocket attack on the town in August.
Since a 50-day war between Israel and Gaza militants in the summer of 2014, a cease-fire has largely held. Sirens wailed in Sderot warning of the incoming rocket, which landed near a school.
Palestinians want a state in the West Bank with east Jerusalem as its capital.
The White House accused Israel of a betrayal of trust Wednesday, in an unusually sharp rebuke over its plans to build hundreds of new settlement homes deep in the West Bank.
The Gaza-bound Zaytouna-Oliva has been seized by the Israeli Navy.
Lieberman added that all fire from Gaza into Israeli territory “will meet a powerful response”.
But the practice has only accelerated since then, Washington says, with new housing blocks being approved, local administrative boundaries moved and unauthorised outposts retroactively approved.
Meanwhile on Wednesday, Israeli forces bombed several areas in the Gaza Strip.
Hamas spokesman Fawzi Barhoum urged global activists to continue sending flotillas to Gaza. “Hamas stresses it cannot keep silent if the escalation continues”, he said.
Wednesday’s incident was the latest in a series of flotillas aimed at breaking through Israel’s naval blockade of Gaza.
“We strongly condemn the Israeli aggression against the global flotilla that tried to break the illegal siege imposed by Israel on 1.8 million inhabitants of the Gaza Strip”, Erekat said in a statement calling for their release.
Passengers aboard the ship, which set sail from the Spanish city of Barcelona last month, include Irish Nobel Peace Prize laureate Mairead Maguire, Swedish and Algerian lawmakers, a South African Olympic athlete and a Malaysian doctor. “The visit and the search of the vessel were uneventful”, the statement said.
“Concrete measures and actions against all Israeli settlement activities should be taken in accordance with worldwide law and United Nations resolutions”.
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The Israeli government said on previous occasions that its land and sea blockade of Gaza was aimed at preventing Palestinian fundamentalist organisation Hamas from getting weapons and supplies.
