The army has sliced the occupied territory of Gaza into three sections with a series of blockades after five Israeli soldiers were killed in a resistance attack on Sunday.
The soldiers died after a bomb was detonated in a tunnel under a military base in south Gaza.
Medics said Mustafa al-Sawarka, 32, was shot on Wednesday while trying to slip across the Mediterranean coast road, blocked off by troops near Netzarim settlement as part of the security clampdown.
Another Palestinian man was seriously wounded in a second shooting incident at the same spot shortly afterwards, witnesses said.
An Israeli military source said soldiers had fired warning shots in the direction of Palestinian cars that sped into a closed military zone along the road, but that none was targeted directly.
After a brief period of relative calm in Gaza after the 11 November death of Palestinian President Yasir Arafat, violence resurged last week with several deadly incidents.
Israel tried to kill a senior fighter in a helicopter missile strike that failed, while Palestinian armed groups resumed peppering settlements with mortar and rocket fire.
A mortar attack killed a female Thai farm labourer and wounded two others in the Ganei Tal settlement on Tuesday.