There were no immediate reports of casualties in the attack.
The sirens were sounded just hours after police captured two individuals from Gaza’s Islamic Jihad group who had escaped from a maximum-security Israeli prison earlier this week.
Early on Saturday, The Jerusalem Post reported that two more escaped prisoners have been captured. They were identified as Zakaria Zubeidi and Mahmoud al-Arida.
The recent rise in cross-border violence tests a fragile truce that ended fierce fighting in May.
More than 260 Palestinians, many of them civilians and children, and 13 Israelis were killed in the May assault on Gaza, during which Israel carried out relentless air raids across the coastal enclave, prompting Gaza fighters to fire rockets towards Israeli cities.
Israel keeps Gaza under blockade, tightly restricting movement out of the territory that is home to two million Palestinians.
Egypt also maintains restrictions on the enclave. Both cite threats from Hamas for the restrictions.
The blockade restricts the movement of goods and people in and out of Gaza and has ravaged the territory’s economy and harming the population of two million.