There were no immediate reports of casualties in the strike in Gaza's Zaitun neighbourhood early on Wednesday.
Palestinian witnesses said three missiles hit the workshops in the nighttime strike.
The last time Israeli helicopters fired on Gaza, Palestinian resistance fighters retaliated by firing home-made missiles on the Israeli town of Sderot, east of Gaza.
Late on Tuesday, Palestinian fighters responded to the Israeli assassination of local leader Numan Tahaina by firing Quds-1 rockets into the Israeli town of Sderot, Aljazeera reported.
An Aljazeera correspondent reported that Tahaina, 38, was on Israel's most-wanted list since the first Palestinian intifada against Israeli occupation in 1987.
Israeli officials admitted they killed Tahaina after firing on his car which refused to stop at an impromptu checkpoint.