On his way back from a trip to several Arab countries, Abbas said "the plan is totally rejected," the Ramallah-based al-Ayyam Daily reported.
"I don't believe that carrying out such measures by the Israeli government would bring on peace or security, instead it puts obstacles on the road to peace," said Abbas.
The Israeli cabinet approved a new route for its West Bank barrier on Sunday. The revised route means that some 55,000 Palestinian residents of east Jerusalem will be separated from the rest of the city.
The number includes more than 3,000 school children, who will have to pass through the fence in order to get to their schools.
Israel's Haaretz said on its website that the decision, which dramatically changes the demographics of Jerusalem, was made despite strident Palestinian objections and some US misgivings.
The route not only cuts off tens of thousands of Palestinian residents of the capital, but also places the largest West Bank settlement, Ma'aleh Adumim, with almost 30,000 residents on the Jerusalem side, it added.