The missile attack early on Sunday destroyed a metal workshop in al-Amal area of the camp, injuring two people, Palestinian security sources and witnesses said.
It was the second Israeli air strike on Khan Yunus in a little more than 24 hours.
Samir Abu Shammalah, Aljazeera's correspondent in Palestine, said an Israeli Apache helicopter fired at least one missile on Sunday morning at an aluminium workshop in al-Amal neighbourhood west of Khan Yunus.
The strike caused major damage to the workshop and a nearby house.
Early on Saturday, Ali Abd Allah, a 60-year-old Palestinian man, was killed and five others were wounded in a similar raid.
Aljazeera reported witnesses as saying Saturday's missile was launched by an Israeli helicopter that landed near a mosque in the Khan Yunus camp.
Palestinian medical staff try to
save the life of Ali Abd Allah
Israeli occupation forces said the missile was targeted at a resistance group planning rocket attacks on a nearby settlement.
After the missile strike, 14 tanks and three bulldozers moved into the camp and began tearing down houses, leaving many homeless.
Izz al-Din al-Qassam Brigades, the military wing of the Palestinian resistance group Hamas, said that they had blasted two Israeli bulldozers advancing into Khan Yunus.
In a statement released on Sunday, the group said they fired an anti-armour Battar missile at one of the tractors at 1.10am, while another missile was fired at dawn at a second bulldozer.
The Israeli attacks came a day after an Israeli woman was killed in a Palestinian mortar strike on an illegal Jewish settlement in the area.
The mortar attack on Friday marked the first time a resident of a Jewish settlement in Gaza was killed in Palestinian shelling, and was expected to mobilise further opposition to Israeli Prime Minister Ariel Sharon's withdrawal plan.
Israel frequently targets metal workshops and foundries in Gaza which it says are used by fighter groups to make mortars and primitive rockets fired against Israelis.
Wail al-Dahduh, Aljazeera's reporter in Gaza, said going by official Palestinian statistics, 50 house were demolished by Israeli occupation forces on Saturday, and dozens of Palestinian families were made homeless.
Thousands of Palestinians have been made homeless by Israeli house demolitions in Gaza in the last four years of fighting.