Zohair al-Qaisi, secretary general of the Popular Resistance Committees (PRC), was attacked because he was planning an attack, the Israelis said.
Another militant was killed with him. The Islamist Hamas movement which runs Gaza said at least eight more died in later Israeli air strikes.
The Israeli military said dozens of rockets were fired into Israel.
A spokeswoman said the rocket attacks had injured at least four people, one seriously. Some of the rockets had been intercepted by Israel’s “Iron Dome” anti-missile system, she added.