The raids took place before dawn on Thursday. There were no immediate reports of casualties.
Witnesses told Al Jazeera that the attacks damaged several houses near one of the targeted sites in the al-Bureij refugee camp in central Gaza.
Earlier in the night, a rocket fired from Gaza struck southern Israel, causing slight damage to a house but no injuries, Israeli police confirmed. Four more rockets were also fired from Gaza, the Israeli military added, following its raids on the besieged coastal enclave, but were intercepted by air defence systems.
No Palestinian faction claimed responsibility for the rocket launches.
In a statement, Hamas, the group that governs Gaza, said Israel’s bombing will only encourage Palestinians to “resist the occupation and step up their support for Jerusalem and its people”.
A surge of violence in Israel and the occupied Palestinian territory has raised fears of a slide back to wider conflict, after last year’s 11-day Israel-Gaza war, in which more than 250 Palestinians in Gaza and 13 people in Israel were killed.
In March, Israeli forces killed at least 29 Palestinians in raids on the West Bank after 14 people in Israel were killed in street attacks.
Israeli riot police also stormed the Al-Aqsa mosque compound – a site revered by Muslims and Jews – last week, wounding at least 158 Palestinian worshippers.
Tensions this year have been heightened in part by the Muslim holy month of Ramadan coinciding with the Jewish celebration of Passover.
Palestinians accuse Israel of encroaching at Al-Aqsa by allowing Jewish worshippers into the sacred compound. They say the move is a violation of a centuries-old policy under which non-Muslims may visit, but not pray.
Israeli leaders have announced they are ensuring freedom of worship for all religions in Jerusalem.
Al-Aqsa is the third holiest site in Islam and is also revered by Jews as the location of two ancient temples.
Palestinians want occupied East Jerusalem, including its Muslim, Christian and Jewish holy sites, as the capital of a future state.
Israel, which annexed East Jerusalem in a move not internationally recognised after capturing the area in a 1967 war, regards all of Jerusalem as its eternal capital.