The sources said that another five people were injured in the incident.
The IDF confirmed targeting Hamas gunmen, but said that the missile was fired from an army helicopter at a Palestinian armed with an anti-tank missile.
According to the Palestinians, an IDF force operated in the southern part of the Strip, between Khan Younis and Rafah, and soldiers have taken over some houses and conducted searches inside.
Islamic Jihad's military wing, the al-Quds Brigades and Izz al-Din al-Qassam Brigades reported that their operatives fired mortar shells at the IDF forces.
Later three Palestinian gunmen were injured when an aircraft fired a missile near an area where troops were operating in the southern Gaza Strip, gunmen and witnesses said.
The three are gunmen of the Islamic Jihad, the group said. Their condition was not immediately known.
Meanwhile, Palestinian terror groups launched two Qassam rockets from northern Gaza towards Israel on Thursday morning. The rockets landed in open areas in the western Negev, one near a gas station.
No injuries or damage were reported.
Hanan Greenberg and AP contributed to the report