There were no reported casualties from the attack an Israeli army spokeswoman described as against a weapons manufacturing plant used by Hamas resistance fighters to produce rockets fired at Israel.
Palestinian sources described the building damaged in the blast as a metal foundry.
The attack followed continued rocket fire on the Jewish state by Gaza fighters on Monday.
Israel has stepped up air raids against Palestinian fighters in response to increased rocket fire recently that has mainly targetted the southern Israeli town of Sderot.
Sderot is the hometown of Amir Peretz, the Israeli defence minister.