A drone was launched from Lebanon at Benjamin Netanyahu's holiday home, his officials said.
The Israeli prime minister was not in the house or in the vicinity at the time of the attack and no one was injured.
Three drones flew into Israeli airspace on Saturday morning, the IDF said.
Two were shot down by defensive barrages.
The IDF added: "One additional UAV hit a structure in the area of Caesarea. No injuries were reported.”
Benjamin Netanyahu owns a holiday home in Caesarea, which is an affluent resort town in the centre of the country.
Meanwhile Israel has launched a wave of airstrikes in Gaza killing at least 50 people including children, according to hospital officials in the strip.
At least ten people including two children were killed when a house was hit in the town of Zawayda, the al-Asqa Martyrs Hospital said. Another 11 people were killed in the Maghazi refugee camp. Another three homes in Jabaliya killed at least 30.
The Palestinian Health Authority said strikes had also damaged two hospitals.
Last week the IDF released footage of the final moments of Yahya Sinwar, widely believed to be the organiser of the October 7 attack on Israel in which more than 1,200 people were killed and over 100 hostages taken,
The video shows the Hamas leader in an armchair as he is spotted by a military drone. He appears to wave a stick at the drone before an Israeli tank shell rips through the building killing him
Sinwar, 61, was said to have spent much of his time hiding in the tunnels under the Gaza Strip.
In a statement, the IDF said its operations in recent weeks in the south had "restricted Yahya Sinwar's operational movement as he was pursued by the forces and led to his elimination".
A White House statement after the death said the Hamas leader’s death could pave the way to a ceasefire.
It said: “There is now the opportunity for a “day after” in Gaza without Hamas in power, and for a political settlement that provides a better future for Israelis and Palestinians alike. Yahya Sinwar was an insurmountable obstacle to achieving all of those goals. That obstacle no longer exists. But much work remains before us.”
