The Israeli military said the target was a structure used by Palestinian fighters to make and store rockets that are fired at Israel. Ambulances raced to the scene, but apparently no one was hurt.
Palestinians said the target was a training facility of the Popular Resistance Committees.
Another missile hit a street in northern Gaza, witnesses said. No one was hurt
The Israeli military noted that during the previous day, fighters fired nine rockets at Sderot, a town just across the Gaza fence, wounding an Israeli civilian.
The Israeli military said the airstrikes were in response to the barrage.
Earlier, the PRC claimed responsibility for firing the rockets at Israel on Tuesday.
Palestinian police said one of the missiles fired at the Gaza building failed to explode, and they were searching for it in a fiend used for training exercises by the fighters.
The facility has been targeted before, and four fighters from the PRC were killed there in an Israeli raid last month.