No injury or damage was caused in any of the incidents.
The Islamic Jihad claimed responsibility for the attacks.
Two Qassams landed in open fields near Sderot, one landed near a kibbutz in the Sha'ar Hanegev Regional Council in the Negev and two landed south of Ashkelon.
Wednesday morning's Border Guard operation in Jenin, in which three Islamic Jihad members, including the group's commander, were killed, have put Israel's southern communities on alert for fear of retaliation.
Civilians were instructed to avoid crowded areas. Despite warnings, Sha'ar Hanegev Council head Alon Shuster said the council did not wish to disrupt daily routine.
In Sderot, records have been complied over the past few weeks of the homes of elderly and disabled residents, in order to prepare for their evacuation if need be.
'Israel may not be able to sit idly by'
On Tuesday, parents of children in Sderot kindergartens received letters urging them to prepare emergency bags for their children.
Shuster said he still does not understand how the government could cancel benefits for Sderot and other Gaza vicinity communities, which include reduced property tax rates, at such a crucial time.
He also said that the fortification of the towns has not yet been completed; while works are progressing in schools, the fortification of residents' homes is still in planning.
On Tuesday, Defense Minster Amir Peretz said in a visit to the area, that Israel may not be able to sit idly by for much longer.
"There is no reason to let anyone turn this escalation into a real threat on the State of Israel. We are certainly doing all we can to ensure that the ceasefire remains," he said.