The Palestinian interior ministry in the Gaza Strip was hit setting the building ablaze and causing serious damage. It's not known if anyone was injured in the attack.
The Israeli military confirmed its planes hit the office of Interior Minister Said Siyam, which it called "a meeting place to plan and direct terror activity".
The Interior Ministry is nominally in charge of Palestinian security forces, although moderate Palestinian President Mahmoud Abbas has removed most of its authority.
In an earlier attack a missile damaged a Palestinian national security post, located near an electricity power station near the Nuseirat refugee camp in central Gaza.
The Israeli military has now launched six air strikes, including four in central Gaza and another further north which were aimed at preventing the abducters of Israeli soldier Gilad Shalit from moving from their present location.
Israel has called a halt to a planned incursion into the northern Gaza Strip amid international appeals for diplomatic efforts to free 19 year old Shalit who was captured during a raid by Palestinian militants.
The pause came after Israel seized dozens of Hamas ministers and officials in an impasse that has threatened to spiral into regional conflict.
The body of a Jewish settler kidnapped by gunmen was also found dumped in the West Bank adding to the tensions.
It’s the worst crisis between Israel and the Palestinians since the radical Islamist movement took office in March.
"It is not a government it is an organisation of killers with a leader in
Damascus," charged Israeli Infrastructure Minister Benjamin Ben-Eliezer, referring to Syrian-based Hamas political supremo Khaled Meshaal.
G8 urges restraint
Meeting in Moscow, foreign ministers of the G8 group of industrialized nations called on Israel to exercise the "utmost restraint".
"The detention of elected members of the Palestinian government and legislature raises particular concerns," the ministers said, adding that they also wanted to see "immediate measures to liberate the abducted Israeli soldier".
Israel, which has a force of about 5,000 troops massed on the border, has launched its biggest military operation since pulling out of the Gaza Strip in September.
Air strikes were carried out on a car in Gaza City but the targeted Islamic Jihad militants managed to escape.
The army was also on high alert on its northern border after Israeli planes flew over Syria in a blunt warning to arch enemy Damascus.
The multi-pronged action came after Prime Minister Ehud Olmert warned he was prepared to take "extreme measures" to bring back Shalit.
In the West Bank, Israeli troops rounded up more than 64 Hamas members, including eight ministers, a third of the Palestinian cabinet, and 24 lawmakers in a vast military sweep overnight.
Some were blindfolded and handcuffed as they were arrested, Palestinian sources said.
Hamas, boycotted by Israel and the West as a terrorist group, condemned the arrests as a declaration of "open war" aimed at destroying its government.
Meeting cancelled
Palestinian leader Mahmud Abbas has appealed for urgent international intervention.
Artillery units and gunboats shelled Gaza on and off throughout the day and more troops crossed into the south, the area where Shalit is believed to be held.
There was no word on Shalit, although the group which claimed to have killed the settler issued another warning to Israel about the soldier's fate.
"Olmert and (Defence Minister) Amir Peretz will be entirely responsible for the life of the captured soldier if the aggression continues," Abu Abir, a spokesman Popular Resistance Committees said.
In a sign of the sharp deterioration in relations with the Palestinians, a meeting to prepare for a summit between Mr Olmert and Mr Abbas was cancelled.
It would have been their first formal meeting since the election of Hamas, which has long advocated the destruction of Israel although this week it signed up to a political initiative that implicitly recognizes Israel.
Shalit's captors have vowed not to release him until all Palestinian women and children are freed from Israeli jails, a demand rejected by Mr Olmert.