Even as the military affirmed it still intended to uphold the truce, it announced it had carried out another air strike in the strip's north where it said weapons had been stored.
Medics said two people were killed in that attack.
The killing of an Israeli soldier in the Gaza Strip on Tuesday has triggered the worst escalation in the enclave since the ceasefire came into effect on October 10.
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 denied blame.
Israel described its latest attack on Wednesday as a targeted strike in the area of Beit Lahia in the north of the strip, where it said weapons had been stored.
It said it would continue to uphold the ceasefire agreement while responding firmly to any violation.
In response to the soldier's death, the military launched what it described as strikes targeting dozens of Hamas militants across the enclave as well as weapons depots and tunnels belonging to the group.
It named 24 militant targets, including one it described as a Hamas commander who took part in an attack on a kibbutz during the October 7, 2023 assault on southern Israel that triggered the war.
The Gazan health ministry said that 46 children and 20 women were among the 104 people killed in the Israeli air strikes.
Reuters could not immediately verify the numbers but Reuters video showed several bodies of women and children inside a hospital during funeral processions.
Despite the bombardments, US President Donald Trump said the US-backed ceasefire was not at risk.
"As I understand it, they took out an Israeli soldier," Trump told reporters aboard Air Force One.
"So the Israelis hit back and they should hit back. When that happens, they should hit back," he added.
"Nothing is going to jeopardise" the ceasefire, Trump said.
"You have to understand Hamas is a very small part of peace in the Middle East, and they have to behave."
Qatar's Prime Minister Sheikh Mohammed bin Abdulrahman al-Thani said on Wednesday that the attack on the Israeli soldier and the subsequent Israeli air strikes had been "very disappointing and frustrating for us".
Qatar, along with Egypt and the US, has been leading efforts to broker peace in the Gaza Strip.
Speaking at the Council on Foreign Relations in New York, al-Thani said Hamas militants had been clear they were prepared to give up governance of the enclave, which they have run since 2007.
Qatar was pushing them to acknowledge they need to disarm, he said.
Hamas denied responsibility for the attack on Israeli forces in Rafah, in the south of the Gaza Strip, and said in a statement that it remained committed to the ceasefire deal which went into effect on October 10.
