A Palestinian protester uses a slingshot to throw stones at Isreali forces during a demonstration at the Israel-Gaza border, east of Khan Yunis in the southern Gaza Strip on August 24, 2018.
Islamic Jihad claimed responsibility for the rockets, saying in a statement that they were in retaliation for the Israeli army's killing of five Palestinian protesters on Friday.
The fresh violence could also scupper hopes of a deal to end the months of increasing tensions.
It said the Iron Dome intercepted approximately 10 of them, while two rockets came down inside the Gaza Strip and the others hit "open areas".
The Israeli army said some suspects briefly crossed the fence.
Defense Minister Avigdor Liberman met with IDF Chief of Staff Gadi Eisenkot and other top security officials on Saturday.
Israeli aircraft struck around 95 sites, including weapons manufacturing facilities and military compounds including Hamas's security services headquarters, it said. The Palestinian Health Ministry estimates the number of Palestinian fatalities at over 200 people since March.
A sixth died when a hand grenade he was holding exploded accidentally, witnesses said.
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The flare-up began after the four Palestinians were killed by Israeli troops on Friday during weekly protests along the border.
The majority have died during protests, while smaller numbers have been killed by air strikes or tank fire.
A fifth Palestinian was killed in the West Bank during clashes with the IDF.
Gen. Ronen Manelis reiterated that Israel considers the terror group responsible as Gaza's rulers.
In recent weeks, the situation along the border has grown more precarious, as indirect negotiations between Israel and Hamas - with the Egyptian military and United Nations acting as intermediaries - have reached a critical turning point.
Israel in response struck dozens of targets in the Gaza Strip on Saturday.
Israel rarely acknowledges it has reached a truce with Gaza's militant groups, which it designates as terrorist organisations.
"We will abide by the cease-fire if the enemy does the same", the Gaza-based militant group said in a statement, while also vowing to "protect the resistance and its position that if attacked will respond to blood with blood".
But Hamas maintains it wants a full lifting of a crippling blockade Israel and Egypt imposed on Gaza to isolate the Islamic movement.