Israeli helicopters fired missiles at an office of Palestinian President Yasser Arafat's Fatah movement and that of another faction in Gaza City early today.
Medics said the Fatah building and offices of the Democratic Front faction were empty at the time and there were no casualties.
An Israeli military statement said the missiles struck two offices "which served as focal points for Palestinian terrorist activity" in the raid close to the site of an ambush that killed six soldiers a week ago.
The Fatah-linked militant group, al-Aqsa Marytrs Brigades, called on supporters "to launch painful strikes against the enemy" in revenge for the missile strike.
Elsewhere in Gaza, Israeli soldiers shot dead at least three Palestinians suspected of seeking to infiltrate into Israel to plant explosives, Israeli media reports said.
Israel's army chief Mr Moshe Yaalon threatened yesterday to destroy hundreds of Palestinian refugee homes after the Supreme Court cleared the way for demolitions in a flashpoint Israeli-held corridor on the Gaza-Egypt border.
Within hours of the court ruling, dozens of Israeli armoured vehicles massed outside Rafah, and hundreds of Palestinians fled their homes, witnesses said.
Rafah was the site of two other deadly ambushes that killed seven other soldiers last week. Mr Yaalon told the cabinet "hundreds of houses" believed to be concealing tunnels or to have been used by gunmen had been marked for destruction.