"This shows the occupation's desire to escalate," said Sami Abu Zuhri, a spokesman for Hamas, which rules the Gaza Strip. "We warn the occupation against continuing this foolishness."
Israel said it targeted two Hamas weapon manufacturing facilities after Gaza militants fired two rockets and following attempts by Palestinians to violently cross the border.
One of the rockets had hit an open field in southern Israel and the other was intercepted.
After days of unrest in annexed east Jerusalem and the occupied West Bank, Gaza has been drawn into the violence since Friday, with clashes along the border leaving nine Palestinians dead, including teenagers, from Israeli fire.
The escalation in violence in the past week has led to mounting fears that Palestinian unrest was spiralling toward a wider uprising, or third intifada.