Ceasefire undermined'
Israeli officials confirmed the raid, saying that they had intended to make arrests but opened fire when they saw that three of the militants were armed with assault rifles.
They blamed the Islamic Jihad militants for attacks on Israelis.
Palestinian officials from Islamic Jihad and Hamas denounced the operation.
"Islamic Jihad and the other resistance groups have the right to respond in any place to this crime of assassination and all options are open," said Dawud Shihab, an Islamic Jihad leader in Gaza.
"What the enemy has done undermines any talk of a ceasefire," he said.
Earlier on Wednesday, Israeli troops shot dead an Islamic Jihad militant near the northern West Bank town of Tulkarm.
There had been a lull in the Gaza violence over the last few days, with the Israeli military reducing operations in Gaza on Monday following a sharp drop in rocket fire from Palestinian militants.
Egypt has been working to broker an agreement.
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