The first air strikes on the southern Gaza city of Khan Yunis killed a militant of the Islamic Jihad and wounded another man, Palestinian sources said.
The Israeli military confirmed the attack, saying it had targeted a member of Islamic Jihad who "was involved in planning a massive attack in the heart of Israel."
"This operation disrupts the execution of the attack by Islamic Jihad," an Israeli army spokeswoman said.
"That organisation has been involved in the firing of rockets towards Israeli territory and Israeli army in the past few days," she added.
Adham Abu Selmiya, spokesman for the Hamas-run health services in the Gaza Strip, named the dead man as 25-year-old Mohammed Jamil Al-Najar.
The Al-Quds Brigade, the armed wing of the Islamic Jihad militant group, said Najar was a member and pledged revenge for the attack.
Later raids hit three sites used by Hamas security south of Gaza City and also a training base of the Islamic Jihad group in Khan Yunis, but caused no further casualties, Hamas officials and eyewitnesses said early Wednesday.
The Hamas facilities housed offices of the Hamas National Security Service and its naval wing, they said.
An Israeli military spokesman confirmed only that aircraft had hit three "terror targets" in response to recent rocket and mortar fire from Gaza.
In the most recent incident a rocket fired from Gaza hit open ground in the Negev desert, causing no casualties or damage.
On Tuesday night, Netanyahu warned of the consequences if the rocket fire were to continue.
Israel launched the devastating "Operation Cast Lead" in December 2008 in response to hundreds of rockets fired from Gaza into its territory.
The 22-day war, which ended in a ceasefire on 18 January 2009, killed 1,400 Palestinians, around half of them civilians, and 13 Israelis, 10 of them soldiers.