"In any event, Maale Adumim and Gush Etzion will be included inside the security fence," Mofaz told reporters.
"We will not return to lines of 1967," he added in reference to the internationally-recognised borders of the West Bank which has been occupied by Israel since the end of the 1967 Six-Day War.
Maale Adumim, which lies close to Jerusalem, is the largest of the West Bank settlements with some 28,000 residents, while around 12,000 live in the 15 settlements which make up Gush Etzion in the Bethlehem region of the southern West Bank.
Both were widely expected to be included in the route of the barrier which is being reworked following a recent high court decision which said its path infringed the fundamental rights of tens of thousands of Palestinians living near Jerusalem.
Israel says the barrier is essential for security reasons but Palestinians argue that the route, by jutting into the West Bank, is proof of an intent to prejudge the borders of their promised future state.
The International Court of Justice ruled last month that any parts built on the Palestinian side of the border were illegal and should be torn down. But Israel has vowed to ignore the judges' non-binding verdict.
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