More than 20 other cases objecting to the route have yet to be decided
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The Israeli High Court has issued a temporary order halting work on part of the West Bank barrier.
The ruling - which comes a day after the court ordered another section north of Jerusalem to be re-routed - applies to a stretch south of Jerusalem.
The latest order follows a petition by Palestinian villagers who say they will be trapped in a loop of the barrier if it is built according to plan.
Several other similar petitions have also been lodged.
The new court ruling applies to a section near Har Homa, or Jabal Abu Ghneim.
Legal precedent
Government officials say they fear the legal objections could lead to lengthy delays in the barrier's construction.
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Guide to the route and structure of the West Bank barrier

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Wednesday's decision by the court to change to the route of the West Bank barrier to alleviate Palestinian suffering has set a precedent for other legal disputes,
says the BBC's Barbara Plett in Jerusalem.
In total, the complex of fences, concrete walls and trenches is planned to run for about 640km (400 miles).
Israel says the barrier is necessary to keep out suicide bombers; Palestinians call it a land grab that divides people from their families, jobs and schools.
The decision comes before a non-binding ruling by the top United Nations court on the legality of the controversial network of fences and walls.
The International Court of Justice, which was asked to examine the issue last December amid mounting international concern, has said it will release its findings on 9 July.