Troops are searching for remains of the aircraft in the north of the Negev desert. It is not clear where it came from.
Local media quoted officials as saying the aircraft flew in from the west, but not from the Gaza Strip.
It was intercepted at around 10:00 local time.
The Israeli Defence Force said it was examining the aircraft’s flight path and whether it was being used for reconnaissance or for a potential act of terrorism.
However, Israeli radio quoted a military spokesman as saying it was not carrying explosives.
Correspondents say several small drones have penetrated Israeli territory in the past, but from the north.
On at least three occasions unmanned aircraft operated by the Lebanese Shia movement Hezbollah were detected.
An Israeli navy ship was damaged by an explosive drone in July 2006.
Two others flew over part of northern Israel in 2004 and 2005 without being intercepted.
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