The court's decision on Thursday stemmed from a petition filed by an Israeli human rights group - the Centre for the Defence of the Individual.
The group is asking Israel's High Court to determine the legality of parts of the barrier that slice into Palestinian territory in the West Bank.
"Three judges will discuss the legality of the fence within a month from today," a court spokesman told journalists. It was unclear when a three-judge panel would rule in the case.
Israel says the wall of wire, concrete and trenches is needed to stop Palestinian bombers. Palestinians say it is a land grab designed to pre-judge borders that should be decided in negotiations.
The barrier's legality is to be debated before a similar hearing at the International Court of Justice (ICJ) in the Hague that begins deliberations on 23 February.
In response to a request by the UN General Assembly, the ICJ will rule on whether Israel was legally obliged to tear down the barrier.
The International Court of Justice
will hear the case in late February
Although the court can give an advisory opinion, it has no legally binding effect.
Taking it personally
Israel remains opposed to plans to debate the controversial West Bank security barrier in the international court, Foreign Minister Silvan Shalom told his Irish counterpart on Thursday.
"This subject should be sorted out through political channels and not in the International Court," Shalom said at a joint press conference with Irish Foreign Minister Brian Cowen.
"The Palestinian decision to take the [barrier] issue to the International Court of Justice in The Hague was a bad decision, a decision which, of course, hurts the possibility of building relations between us and them."
Israel is expected to argue the barrier is crucial to the future security of the Jewish state when it makes its case to the court in late February.