The exchange rattled an uneasy truce between the two sides Israel and Gaza brokered after a spike in hostilities.
The Israeli military said the targets of the multiple air raids in the southern Gaza Strip included a weapons manufacturing facility. There were no reports of injuries.
The air attacks came shortly after Israeli Prime Minister Benjamin Netanyahu threatened to “respond vigorously to any attack.”
“If someone in Gaza thinks that he can raise his head after Operation Black Belt, he is sorely mistaken,” Netanyahu said in a statement, referring to two days of exchanges between Israeli forces and Palestinian fighters two weeks ago that was the worst such cross-border conflict in months.
Late on Tuesday, the Israeli military had said it identified two projectiles fired from the Gaza Strip, with missile defences intercepting one.
The attack was the second incident this week, and rattled the shaky ceasefire brokered by Egypt and the United Nations earlier this month that ended the latest round of fighting.
The flare-up was triggered when Israel killed a senior Islamic Jihad commander in Gaza. The fighter group launched hundreds of rockets at Israel in response. Israeli retaliatory attacks killed at least 34 Palestinians, including 16 civilians.
Unofficial ceasefires have led to months of calm between Israel and Hamas, which has ruled Gaza since 2007.