The airstrike is thought to be one of the fiercest attacks since a ceasefire was agreed in November.
However Israel's defence minister earlier this week gave the army permission retaliate to any insurgents firing rockets into the Jewish state.
An Israeli army spokesperson told the news agency that the attack was launched due to militants planting bombs near the border.
"The army has found 40 explosives planted in that area since the November ceasefire," the spokesman said.
Israeli security sources also believe armed Hamas supporters have been upgrading their weapons and digging tunnels in preparation for a possible attack.
However today's airstrike comes amid high tensions in the region as the fragile Palestinian unity government remains less than one month old.
Clashes in the Gaza Strip on Friday between members of rival parties Hamas and Fatah saw two militants and a young boy wounded.
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