Terrorist groups in the West Bank and abroad have intensified efforts to smuggle explosives over Israel's borders.
An IDF engineering vehicle was hit by an explosive device during the raid.
Following recent use of IEDs in attacks, most notably in a blast near Joseph's Tomb, commandos warned it "will only get worse" in the West Bank.
Despite the violence, the visit to Joseph's Tomb continued as planned.
The thwarting of a weapons smuggling attempt from Jordan was originally announced by the IDF in July.
The soldiers arrested one of the armed terrorists who had been injured in the exchange. The weapon he used to fire at the IDF soldiers, an M-16, was confiscated.
"There are nine deaths now, but there may be more as unidentified human remains have been found," Narathiwat's governor Sanan Phongaksorn said.
The EFP has the stamp of the Iranian octopus on it, an octopus now saying it wants to try to do to Jenin what it did to the region.
Israel Police said on Sunday that the fight against crime and violence in the Arab sector was their top priority.
Heavy fighting between IDF soldiers and Palestinian gunmen left at least three Palestinians dead and 28 injured.
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