Israel's High Court ordered the military on Thursday to reconsider the route of a portion of its security barrier, which was to pass through the West Bank village of Battir, an environmental NGO said.

"The High Court this afternoon... ordered the military to present an alternative plan within 90 days," the Friends of the Earth Middle East (FoEME) group said.

"We are convinced that, due to the unique nature of the area under discussion, there is a need for the security officials to reconsider, in particular as regards the nature of the barrier and security arrangements of the problematic areas," the group quoted the court decision as saying.

The route of Israel's barrier in the West Bank has been challenged on multiple occasions, but the court decision comes after an unusual coalition jointly contested the portion due to pass through Battir.

FoEME, along with residents of the village and the Israeli Nature and Parks Authority, argued that that the planned route would damage a network of ancient terraces in Battir, calling on the court to force a reroute.

Battir, located west of Bethlehem, is famous for the terraces dating back thousands of years that the Palestinians hope will receive UNESCO World Heritage status next year.

Israel's defence ministry said the ruling referred to a 500 metre (yard) portion out of six kilometres (3.7 miles) of barrier in the Battir area.

"The defence establishment will reconsider these 500 metres in accordance with the high court decision and will present its stance to the court in due time," it said.

"The defence establishment once again emphasises the security necessity of this part of the fence," it continued. "This particular route has been designed for security purposes and to prevent the free entrance of terrorists into Jerusalem and the heart of Israel."

The ministry has argued that the route would not damage or affect the terraces, and urged the court to leave the plan intact.

FoEME's Israel director Gidon Bromberg said the group was "delighted" with the court decision.

"The military had failed to bring a single expert in the field of cultural and natural heritage to support their case, yet they constantly claimed that they were striking the right balance between the needs of security and heritage values," he said in a statement.

"We trust that this time the military will reconsider security options based on the advice of heritage experts."