"The IDF [Israeli military] targeted and identified hitting armed Palestinians preparing to fire rockets," the army spokesman said, adding that they were in the same place from which the earlier attacks had been launched.
The Islamic Jihad movement said in a statement that three of their fighters were hit by an Israeli missile in the southern Gaza town of Khan Yunis.
Earlier on Tuesday, an Israeli soldier was wounded when troops clashed with Palestinian fighters in the southern Gaza Strip, the Israeli army said.
Palestinian witnesses said several tanks and bulldozers made an incursion into southern Gaza, east of the town of Khan Yunis and exchanged fire with Palestinian fighters.
The armed wing of Hamas, which has controlled Gaza for nearly a year, said its fighters had fired on Israeli troops and that the "Zionist enemy recognises that one of its soldiers was wounded".
Israel frequently launches raids into the Gaza Strip, which it says are aimed at curbing cross-border rockets fired by Palestinian fighters.
The rockets rarely cause death or injury, but cause panic in southern Israeli communities.