"The projectile, whose exact nature we have not yet ascertained, landed in the Eshkol district" in the Negev desert, an Israeli military spokesperson said.
The Israeli army earlier confirmed that aircraft attacked a total of six targets in Gaza overnight, following a weekend which saw mortar rounds fired into Israel from Gaza.
Hamas, which rules Gaza, said the weekend's barrage had been in response to an Israeli strike last week that killed two of its members.
Also on Tuesday, Israeli troops entered a village near Nablus to reimpose a curfew as they continued searching for killers of an Israeli family.
The village of Awarta was the centre of a massive manhunt in the aftermath of the stabbing death of a couple and their three young children in the nearby settlement of Itamar on 11 March.
Following the murders, troops entered Awarta and imposed a curfew for five straight days, conducting house-to-house searches for the killers.
Around 60 villagers were detained for questioning, but so far no one has been charged, with the military refusing to comment on the operation.