Israel has sealed off the Gaza Strip after six Israelis were killed in an attack by Palestinian militants at a major crossing point.
Thursday night's attack is being seen as a first test for newly-elected Palestinian leader Mahmoud Abbas.
Mr Abbas said the bombing and shooting raid at Karni, and Israeli military actions, "do not benefit peace".
Mr Abbas, successor to the late Yasser Arafat, is hoping to persuade militant groups to agree to a ceasefire.
Joint responsibility for the raid was claimed by three Palestinian groups, including Hamas and the al-Aqsa Martyrs' Brigades, which has links with Mr Abbas's Fatah movement.
Three Palestinian gunmen were killed in the attack at Karni, the main crossing point for food and vital supplies into the Gaza Strip, home to 1.3 million Palestinians.
Israel has closed that crossing point and two other major crossings, Erez and Rafah, until further notice.
However, Israel has indicated that it will hold off from tougher retaliation, to give Mr Abbas - who is being sworn in on Saturday - more time to rein in militants.
Israeli Justice Minister Tzipi Livni told Army Radio: "We must try to strengthen [Mr Abbas] as a leader, assuming that at some time or other he will be able take control of the terror organisations."
Blow for Abbas
Mr Abbas has said previously he will not take on Palestinian armed groups by force, and instead wants to persuade them to agree to a mutual ceasefire with Israel.
Moderate head of main political faction Fatah
Seen as someone Israel will talk to
Willing to talk peace with Israel
Wants end to Palestinian armed uprising
Pledges to stick to key positions of late Yasser Arafat
The BBC's Alan Johnston in Gaza says the involvement of Fatah-linked al-Aqsa Martyrs' Brigades in the latest assault will be a blow to Mr Abbas.
It shows that even some of the militants in his own political camp do not agree that it is time to halt the violence, our correspondent says.
Israel, which has occupied Gaza since 1967, is planning to withdraw its troops and settlers from the territory this year.
But our correspondent says groups like Hamas are very keen to portray the Israeli withdrawal as a retreat under fire.
In Thursday's attack, the Israeli army says a truck was rammed through a wall at the crossing late on Thursday, and then three Palestinian militants ran through, firing their weapons and hurling explosives.
Israeli security guards returned fire and the militants were killed.