The Israeli Defense Forces said it "struck military compounds belonging to the Hamas terror organization, which were used as facilities and meeting sites for terror operatives in Hamas' Khan Yunis and Gaza Brigades," The New York Times reported.
Palestinian news reports said one of the strikes caused property damage but no casualties were immediately reported in Gaza.
IDF said that "terrorist activity took place in the attacked compound," according to The Times of Israel.
"The IDF is prepared for all scenarios, including the resumption of hostilities in the face of continued terror acts from the Gaza Strip," the military said.
Multiple fires broke out in southern Israel with at least 20 sparked by incendiary balloons launched from Gaza, The Jerusalem Post reported.
Three Palestinians were also arrested by IDF after crossing the Gaza border fence into Israel.
The exchange was the first major escalation of hostilities between the two sides since they agreed to a cease-fire last month following 11 days of violence including an Israeli bombing campaign that killed more than 250 people, while at least 13 people in Israel were killed by retaliatory Hamas rocket fire.
Earlier in the day, several Palestinian activists were injured during clashes with Israeli security as Jewish groups, including members of the Israeli Knesset, participated in a right-wing march from Damascus Gate to the Western Wall to celebrate Israel seizing control of the wall during the 1967 Six-Day War.
Bennett, who previously served as defense minister under Netanyahu, in 2019 described those who launch incendiary balloons from Gaza as "terrorists" who should be killed.
"An explosive balloon is like an anti-tank missile," he said. "Whoever launches one is a terrorist who is trying to murder Israelis and must be hit."