Palestinian emergency services said that the raids severely damaged the National Islamic Bank in Gaza City, set up by the strip's Hamas government, in an attack confirmed by the military.
"A financial institution used by Hamas to fuel its terror activity was targeted in the northern Gaza Strip," a military statement said.
An army spokeswoman told AFP that at least three rockets hit southern Israel overnight, and two more were intercepted by the Iron Dome missile defence system.
Monday was the bloodiest day of the Israeli operation since it was launched on Wednesday, with 32 people killed.
The latest violence on Monday night killed a family of four who died in an attack on the northern town of Beit Lahiya, and two teenage brothers who were killed in the southern city of Rafah, bringing the six-day death toll to 109.
During the day, warplanes had attacked Gaza City's Shuruq tower media centre -- the second time the building has been targeted -- killing a senior Islamic Jihad militant.
Islamic Jihad sources named him as Ramez Harb and said he was a senior commander in its armed wing, the Al-Quds Brigades.
The late-night strike on Beit Lahiya killed Fuad Hijazi and his wife Amna and their two children, one aged 4 and the other 18 months, medics said.