"Israel Air Force fighter jets targeted a terror target in a military compound belonging to the Hamas terror organisation in Rafah, southern Gaza Strip," it said in an English-language statement.
The strike on the enclave's Islamist rulers came after four Palestinians "carrying bottles filled with flammable material" breached Gaza's border fence on Saturday evening near the kibbutz of Kissufim, Israeli daily Haaretz reported, citing the army.
There, an army spokeswoman told AFP, they attempted to torch heavy equipment used for work on the frontier barrier.
The machinery was damaged but did not catch fire, and the attackers fled back into Gaza, she said.
No casualties were reported.
"The incident that took place yesterday is one of many severe incidents that have taken place in the security fence area," the statement said.
Israel holds Hamas, which rules Gaza, accountable for all attacks launched from the blockaded coastal territory.
Last month there was an uptick in cross-border violence, seen as among the most serious since Israel and Hamas fought a war in 2014 -- their third since 2008.
After a bomb wounded four Israeli soldiers inspecting the border fence on February 17, Israel responded by pounding 18 Hamas facilities in two waves of air strikes.
Israeli ground forces also killed two Palestinian teenagers in cross-border fire.
Last Sunday, Israel said it had carried out air strikes against an underground Hamas facility in the Gaza Strip, adding that its ground forces had destroyed a partly-built tunnel that could have been used for attacks on Israel.
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