The latest escalation of tension follows weekend border clashes in which dozens were injured.
He added that fighters loyal to the ruling Hamas Islamist movement had fired on the Israeli aircraft.
"A Hamas underground rocket launch site that is located adjacent to civilian homes and a school in Shejaiya, was also struck," it added, saying "the strikes were in response to Hamas launching incendiary balloons into Israeli territory".
They are a common tactic used by Palestinian militants in the Gaza Strip, which has been under a strict Israeli blockade since 2007, when Hamas took power there.
Saturday saw intense hostilities on the border.
An Israeli border police officer and a 13-year-old Palestinian were critically injured.
Over 11 days in May, Israel pounded Gaza with air strikes in response to rockets fired from the enclave.