Israeli warplanes bombed bunkers at a Hamas base in Gaza early Thursday following the first rocket fire from the territory since early May, the military said.
Israeli aircraft targeted "underground infrastructure" at the base in the southern Gaza Strip, it said in a statement.
A Palestinian security source said there had been no injuries.
The strike came after Israeli air defences intercepted a rocket launched from the territory, the first since hundreds were fired in early May in a two-day flare-up which killed four Israelis and 25 Palestinians.
On Wednesday evening, Israel announced it had banned all fishing off Gaza in retaliation for the launching from the enclave of more balloons with incendiary devices attached.
"Due to the continuous launching of incendiary balloons and kites from the Gaza Strip towards Israel, it has been decided tonight (Wednesday) not to allow access to Gaza's maritime space until further notice," the Israeli defence ministry department responsible for Palestinian civil affairs, COGAT, said.
The move came after COGAT said on Tuesday it had reduced the extent of the fishing zone to six nautical miles offshore from 10 nautical miles, having downscaled it from 15 nautical miles a week ago.
A spokesman for the Israeli fire service said incendiary balloons from Gaza caused seven fires on Tuesday alone.
In the past year, Palestinians have succeeded in setting fire to large areas of farmland in southern Israel.
Expanding the fishing zone was seen as a key element of an informal truce agreement reached between Israel and Gaza's Islamist rulers Hamas to restore calm after the May 4-5 flare-up.
Under that agreement, which Israel never publicly confirmed, the Jewish state was expected to ease its crippling blockade of Gaza in exchange for calm.
Bassem Naim, a senior Hamas official, accused Israel in a statement of "evading and retreating from implementing the recent agreements on false pretences, such as the fires surrounding Gaza."
Three human rights groups, two Israeli and one Palestinian, also criticised the closure, saying it punished all Gaza's two million people.
"The sanctions imposed by Israel in Gaza's fishing zone in response to actions over which fishermen in Gaza have no control constitute illegal collective punishment, and must end immediately," they said.
Israel has fought three wars with Hamas and its allies since 2008.
There are concerns that another flare-up could occur ahead of Israel's September 17 elections.