One Palestinian was killed by Israeli shelling overnight and another was shot dead by Israeli forces, WAFA said on Friday.
The Israeli military did not immediately reply to a Reuters request for comment.
A third Palestinian died of wounds suffered from previous Israeli shelling, the news agency reported.
The US-brokered ceasefire, which left thorny issues such as the disarmament of Hamas and a timeline for Israeli withdrawal from the Gaza Strip unresolved, has been tested by periodic outbreaks of violence since it came into place three weeks ago.
Between Tuesday and Wednesday, Israel retaliated for the death of an Israeli soldier with bombardments that Gaza health authorities said killed 104 people.
Israel said on Wednesday that it remained committed to the ceasefire despite its retaliation.
Israel says the soldier was killed in an attack by gunmen on territory within the "yellow line" where its troops withdrew under the truce.
Hamas has rejected the accusation.
Gaza's health ministry said the Red Cross had delivered to it 30 bodies of Palestinians killed by Israel during the war, a day after Hamas handed over two bodies of hostages.
Under the ceasefire accord, Hamas released all living hostages held in Gaza in return for nearly 2000 Palestinian prisoners and wartime detainees, while Israel agreed to pull back its troops, halt its offensive and increase aid.
Hamas also agreed to hand over the remains of all 28 dead hostages in exchange for 360 Palestinian militants killed in the war.
After Thursday's release, it had handed over 17 bodies.
Hamas has said it will take time to locate and retrieve the bodies of all the remaining hostages.
Israel has accused Hamas of violating the truce by stalling in handing over bodies.
Two years of conflict in Gaza have killed more than 68,000 Palestinians, according to Gazan health authorities and left the enclave in ruins.
Israel launched the war after Hamas-led fighters attacked southern Israel in October 2023, killing 1200 people and bringing 251 hostages back to Gaza.
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