The army took control over Mexico's customs points during the changover
Mexico has replaced more than 1,000 customs agents at airports and border crossings with newly trained inspectors in a major crackdown on corruption.
Officials said the agents had been let go after their contracts were allowed to expire.
They said the new 1,400-strong force had been rigorously trained to detect contraband, from guns and drugs to appliances smuggled into the country.
During the changeover, the army took over customs border posts.
"This change is part of our response to new demands in the fight against contraband," Mexico's customs authority spokesman Pedro Canabal said.
He said that the deployment of the new agents would improve Mexico's tax collection, noting that nearly 50% of the country's VAT was collected at customs.
He said the government was also trying to seize more drugs and also guns smuggled in from the US.
Mexican President Felipe Calderon has declared war on the illegal narcotic organisation in Mexico, deploying 40,000 troops to fight the cartels.
Thousands have been killed in drug-related violence in the past few years.
The replacement of the customs officers follows a similar operation in the police force, where thousands have been fired.
Last week, President Calderon was offered lavish praise by his US counterpart Barack Obama for his determined approach to defeat the drug cartels.
The strategy remains broadly popular among Mexicans, the BBC's Stephen Gibbs in Mexico City says.
However he says many are weary of one consequence of the policy: that violence between competing drug cartels and the Mexican authorities confronting them appears to be getting worse.