Mexico's congress has complained that the US Homeland Security secretary, Michael Chertoff, and workers building a border fence crossed into Mexican territory without permission.
Politicians said that earlier this week while on a visit to Arizona, Chertoff and US government workers briefly crossed part of the 2,000-mile (3,200-km) border.
The US ambassador to Mexico, Tony Garza, said Chertoff was not involved in the alleged incident and that recent photos taken of him near the border were from another part of Arizona.
Garza said the US and Mexican governments were investigating whether the workers had actually crossed the border.
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.