Sirens blare in the Hof Ashkelon region of southern Israel, just north of the Gaza Strip, the army says.
The military says it is investigating what triggered the system.
There are no immediate reports of impacts.
Earlier, the Hamas and Palestinian Islamic Jihad claimed that an Egyptian-brokered ceasefire agreement was reached with Israel, due to begin at midnight. A senior Israeli official denied the report.
The latest alarm comes less than an hour after sirens sounded in the city of Ashkelon and in the central Negev in what the army later determined to have been a false alarm.
However, a number of mortar shells were found to have been fired at the Eshkol region, east of the Gaza Strip.