While one missile slammed into a motor parts store on Wednesday, two others destroyed a metal foundry.
Palestinians, however, claimed the targets were just civilian businesses.
Though no one was reportedly killed by the strikes, a six-year-old boy was cut by flying debris.
The Israeli army said in a statement that the targets "were part of the manufacture and supply network of weapons in the Gaza Strip".
Palestinian witnesses and security sources denied the charge.
Earlier during the day, an explosion in the Gaza home of a Hamas leader wounded him and killed five other Palestinians.
While the Palestinian resistance group blamed an Israeli air strike for the blast, the Israelis admitted trying to kill the leader.