Mexican presidential spokesman Ruben Aguilar said that the 1,125 kilometre barrier would create a "climate of tension" along the frontier.
The decision creates "a climate of tension among the border communities and creates splits instead of a convergence between the two countries," he said.
The US Congress on Friday approved construction of the wall along the border, which tens of thousands of mainly Latin American immigrants cross illegally each year.
The barrier is opposed by advocates of an easier immigration policy, but backed by many in the United States who want a crackdown on the estimated 11.5 million illegal immigrants in the country.
Speaking at a gala press dinner, president-elect Felipe Calderon, who assumes office December 1, said "neither decree nor physical barrier" will reduce migration across the border.
"I understand the right of every country to determine its security and protect its territory, but two such clearly and inevitably complementary economies cannot be separated with a wall," said Mr Calderon, of the conservative, pro-business National Action Party.
Responding to criticism of the decision, US Assistant Secretary of State for Western Hemisphere Affairs, Thomas Shannon, asked for patience.
Construction of the wall will be part of a more multifaceted immigration reform, he said at a meeting of the Inter American Press Association.
"We ask you for patience. In the long run, what we will see is that we are going to have a series of measures that will be part of a much broader immigration reform that will not only improve our security, but will also recognize the work of many of those who come to our borders," he said.