The barrier, mostly fence but partly wall, runs in and around the West Bank.
Shalom Sunday met the new United Nations Secretary-General's Middle East Envoy, Alvaro de Soto.
"I would like to warn against the renewed attempts by the Palestinian Authority to transform the United Nations and the U.N. bodies into tools against Israel," Shalom said.
The Palestinian initiative to hold a special U.N. General Assembly discussion on the barrier "is no more than an attempt to internationalize the conflict and to malign Israel," he said. "It harms the positive atmosphere which can and should develop around the Disengagement Plan."
The Palestinian Authority wants to pressure Israel to stop building the barrier, dismantle built-up sections and compensate Palestinians hurt by it. Israeli security officials maintain the barrier has proven its effectiveness by reducing the number of suicide bombings.