The Israeli army said it was targeting two factories used to make weapons, as well as a smuggling tunnel under the border with Egypt.
Dozens of tunnels are said to criss-cross between southern Gaza and Egypt's Sinai desert, providing a lifeline to Gaza residents who are starved of basic supplies due to Israel's blockade of the territory.
Sources say there are more than 6,000 Palestinians employed in the clandestine industry.
The Israeli attacks came just hours after Hamas said it had reached an agreement with other Palestinian armed groups in Gaza, to stop firing rockets into Israeli towns.
Fathi Hamad, the interior minister of Gaza's Hamas-led government, made the announcement on Saturday.
He said the move was aimed at preventing such retaliatory attacks to allow Gazans to rebuild the homes destroyed during Israel's three-week war launched at the end of last year.
"The factions have agreed that nobody should in this time, do any actions of the resistance in the framework of firing rockets," Hamad said.
"But if, in the framework of a clash, if there was an incursion, then the possibility is open for response."
The Israel military offensive on Gaza, which began in December last year and ended in January, left more 1,400 Palestinians dead.
There has been a significant reduction in the number of Palestinian rocket attacks and Israeli air raids since both sides declared unilateral ceasefires following the war.