Mexico sees the barrier, being built along parts of California, Arizona, New Mexico and Texas, as offensive saying it will be ineffective and cause more deaths along the border.
The US says it is needed to stop illegal immigration, terrorism and drug smuggling.
Jorge Zermeno, the speaker of the Mexican lower house, said: "The lower house condemns the violation of Mexican territory by personnel building the metal barrier between the cities of Douglas, Arizona and Agua Prieta, Sonora, who were lead by US Secretary for Homeland Security Michael Chertoff."
Chertoff is due to meet Mexican and Canadian security officials to discuss border security at talks in the Canadian capital, Ottawa, on Friday.
The US secretary of state, Condoleezza Rice, will also attend the scheduled talks.