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The military said the blast went off at about 5:30 a.m., close to a makeshift tent encampment where tens of thousands of Syrian refugees are stranded, awaiting entry to Jordan.
The camp, known as Ruqban, is one of two that have sprung up along an earthen barrier, or berm, which runs along the border in a remote desert area.
A booby-trapped car exploded at the berm, “killing and wounding a number of border guards,” the military said in a statement.
It said several other “hostile” vehicles were destroyed, but did not give further details.
No militant group immediately claimed responsibility for the attack.
The extremist group Islamic State controls large areas in neighboring Syria and Iraq, and Jordan has fortified border defenses to prevent attacks and infiltration attempts.
Jordan has also widened a crackdown on IS sympathizers at home, jailing hundreds in the past two years for promoting the group’s ideas on social media.
The kingdom is a member of the U.S.-led international military coalition against IS.