The air strike on Wednesday came after Palestinian fighters attempted to stop occupying Israeli troops from demolishing Palestinian homes near a Jewish settlement.
Israeli military sources said the army was carrying out an operation against "terrorist infrastructure" in the Khan Yunis camp in the southern Gaza Strip and the helicopter had fired at an "open area" to ward away armed men.
Witnesses said about 10 Israeli tanks, armoured personnel carriers and bulldozers swept into the camp in the night-time incursion, drawing fire from the fighters.
A helicopter then launched a missile which the witnesses said exploded near a group of Palestinians.
Medics said about 15 people were wounded.
Residents fled into the night as Israeli bulldozers demolished homes bordering the Jewish settlement of Neve Dekelim.
Israel has carried out many missile strikes and ground offensives in Gaza and the West Bank to quell the Palestinian uprising since 2000.