Israeli air strikes killed six Palestinians and wounded more than two dozen in 24 hours while Palestinian mortar and rocket fire targeted Israel, sources on both sides said.
The exchanges of fire across the Gaza border raised fears of a fresh descent into violence just 48 hours after militant factions agreed to end rocket attacks on southern Israel on condition the air force also stopped its raids.
The clashes were triggered by an Israeli air strike Monday night that killed Ismael al-Ismar, 34, a leader in the Al-Quds Brigades - the armed wing of the militant Islamic Jihad - in the southern Gaza city of Rafah.
An Israeli military spokesman said it targeted "an activist linked to Islamic Jihad who was implicated in attempted terrorist actions in the Sinai."
Israeli public radio said Ismar funded last week's attacks on southern Israel's border with Egypt which killed eight Israelis and started a wave of tit-for-tat violence that left 15 Palestinians dead and another Israeli.
Cairo, which said five of its policemen were shot dead by Israeli troops and put pressure on the Jewish state to curb its response in Gaza, brokered the truce announced on Sunday.
Several hours after Ismar's death, two mortar shells hit the Eshkol region, which flanks the Israel-Gaza border, Israeli police said.
Al-Quds Brigade said it had fired six shells at the Kissufim border crossing, in response to Ismar's killing.
Immediately afterwards, the air force hit "two terrorists who had fired rockets at Israel," the army said, in a strike which Palestinian medics said moderately wounded two Islamic Jihad militants near Deir al-Balah.
Palestinian medics later reported finding the body of Ismael Amoum, 65, in the same area, saying it had been blown to pieces.
In a third strike, Palestinian medical sources said 20-year-old Attiyeh Moqat had been killed, and the Al-Quds Brigade claimed him as a member. Another Palestinian was wounded, the sources said.
Israeli police said that strike came after four rockets slammed into southern Israel without causing casualties or damages.
The Al-Quds Brigade said it had fired several rockets at Israeli towns, including the large city of Beersheva in southern Israel but the army and police did not confirm the claim.
However public radio said a dozen rockets had been launched, two of them against Beersheva.
And Israeli police said one damaged a public building and another hit a car, slightly injuring a baby inside by flying glass.
The radical Popular Front for the Liberation of Palestine (PFLP) also claimed responsibility for two rockets fired on Israel, while another rocket launched from Gaza struck Egypt and wounded a woman, the official Egyptian MENA news agency reported.
More Israeli air strikes around midnight Wednesday killed three Palestinians and wounded some two dozen in the northern and southern Gaza Strip, Palestinian medical sources said Thursday.
One attack at Beit Lahiya in the north left two dead and 20 wounded, shortly after the air force targeted a tunnel being used to smuggle goods into the southern Gaza Strip near Rafah, killing one Palestinian and wounding three, while another three were missing.
The Hamas government in the Gaza Strip accused Israel of violating the unwritten ceasefire and called for UN intervention.
"Such aggressive behaviour confirms that Israel has no true intention of maintaining the truce and insists on escalating the situation," Hamas said.
Israeli Prime Minister Benjamin Netanyahu convened his security cabinet on Wednesday, public radio said, two days after it had agreed to limit the response to rocket fire from Gaza.
Army chief of staff General Benny Gantz and other security officials told ministers they believed Hamas was trying to enforce the truce and that Islamic Jihad's fire on Wednesday morning was a response to the killing of Ismar, the radio said.
It also quoted a military source as saying Gantz ordered increased personnel and intelligence along the Israeli-Egyptian border.