Hamas said Israel would pay a "heavy price" for the deaths of its militants
Israel says it favours an extension of the truce in Gaza, despite an outbreak of violence in the past two days.
"We hope the truce can be applied again, we believe in it and it looks like things are calming down," said deputy Defence Minister Matan Vilnai.
The five-month-old calm between Israel and Gaza militants seemed in jeopardy after an Israeli incursion and a rocket barrage from the Palestinian side.
A seventh militant was killed in an Israeli air strike on Wednesday night.
Tuesday's overnight raid by Israeli troops was launched to destroy a cross-border tunnel, the military said.
One Palestinian militant from Hamas was killed in the ensuing fighting and another five were killed in air strikes against rocket and mortar crews.
Both Israel and Hamas, which controls Gaza, accused each other of violating the truce, but each have said they hoped there would be no further escalation.
There were no casualties reported from the dozens of Palestinian rockets which pounded southern Israel on Wednesday. Four Israeli soldiers were reported wounded in fighting.
Before the June ceasefire, near daily rocket fire from Gaza had severely disrupted life in southern border towns and correspondents say Israel found no military solution to stop them.
One of the targets for rocket crews was the city of Ashkelon, near Gaza
Israeli air strikes meanwhile killed scores of Palestinians in Gaza in the last 12 months, mostly Palestinian militants.
Mr Vilnai comments to Israeli army radio came hours before US Secretary of State Condoleezza Rice was scheduled to arrive for talks with Israeli officials and Palestinian Authority officials in the West Bank.
The Bush administration - which set an Israeli-Palestinian deal as a top priority before it left office - has just 77 days left to make some mark, although there is widespread scepticism among participants.
Ms Rice is making her eighth trip to the region since the November 2007 Annapolis peace conference which launched the US initiative.
She will also visit the two Arab states which have peace treaties with Israel, Egypt and Jordan.