One of the targets, in the southern town of Rafah, was a facility of the Islamist movement's military wing, the Ezzedine al-Qassam Brigades, the sources said.
The ministry said the attack targeted an observation post belonging to the Palestinian resistance group, the Islamic Jihad.
It did not confirm a second raid.
Israeli tank shelling killed two members of the Palestinian militant group Islamic Jihad and wounded a third in the Gaza Strip on Sunday (May 27), medical officials said, after weeks of border protests that have drawn lethal army fire.
Gaza's Health Ministry says dozens of Palestinians were hurt along the border with Israel.
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The fatalities have been caused by the Israeli fire since March 30, when people in the besieged coastal territory began peaceful rallies near the fence demanding the right to return to their homeland. "We are returning to Palestinian lands".
It added that the strike was also in retaliation for repeated Palestinian attempts to damage the border fence and "security infrastructure" during ongoing border protests.
Low-level demonstrations along the border have continued since protests peaked on May 14, when at least 61 Palestinians were killed as tens of thousands of Gazans protested the U.S. transfer of its embassy in Israel from Tel Aviv to Jerusalem.
No Israelis have been killed in the clashes. The deadliest clashes occurred following the transfer of the U.S. embassy to Jerusalem al-Quds on May 14.
The videos show four terrorists infiltrating into Israel from Gaza, as well as the intense rioting along the border earlier today. It accuses Hamas of trying to carry out attacks under the guise of protests.