The flights will run twice a week from El Paso, Texas, to Mexico City until Nov. 29, at which time both governments will evaluate the results and decide whether to continue. The first flight left Tuesday with 131 Mexicans aboard.
The flights are not voluntary, unlike a previous effort from 2004 to 2011 to deport Mexicans arrested by the Border Patrol during Arizona's deadly summer heat.
The U.S. government will pay for the flights, and the Mexican government will pay to return people from Mexico City to their hometowns, U.S. Immigration and Customs Enforcement said in a news release.
ICE spokeswoman Nicole Navas said Mexicans from that country's northern border states will not be eligible. The Mexican government did not immediately respond to requests for comment Tuesday.
The experiment comes as Mexican cities along the U.S. border are grappling with large numbers of deportees who have no roots, few employment prospects and sometimes limited Spanish. Many are deported to cities that are among the hardest hit by organized crime in Mexico, particularly across the border from Texas in the state of Tamaulipas.
"The newly repatriated, often with no means to return home, are susceptible to becoming part of criminal organizations as a means of survival," Gustavo Mohar, Mexico's interior undersecretary for population, migration and religious affairs, said in a statement released by ICE.
ICE Director John Morton said the flights "will better ensure that individuals repatriated to Mexico are removed in circumstances that are safe and controlled."
ICE, which is managing the flights, said passengers will include Mexicans with criminal convictions in the United States and those who don't have any. They will be taken from throughout the United States to a processing center in Chaparral, N.M., before being put on flights at El Paso International Airport.
President Barack Obama's administration has made migrants with criminal convictions a top priority among the roughly 400,000 people of all nationalities who are deported each year. The Department of Homeland Security said nearly half of the 293,966 Mexicans deported in its last fiscal year had criminal convictions in the United States.
The policy has fueled concern in Mexican cities along the U.S. border that deportees are being victimized, turn to petty crime or are recruited by criminal gangs. In February, Homeland Security Janet Napolitano and Mexican Interior Secretary Alejandro Poire announced plans for a pilot program, which was to begin April 1, but negotiations delayed the start until Tuesday. Homeland Security officials said the time was needed considering the complexities and logistics of the effort.
The Border Patrol will not participate in the flights, which is called the Interior Repatriation Initiative, Navas said.
Under a previous effort, some Mexicans who were arrested by the Border Patrol in Arizona's stifling summer heat were offered a free flight to Mexico City, but they could refuse. The Mexican Interior Repatriation Program flights carried 125,164 passengers at a cost of $90.6 million from 2004 to 2011, or an average of $724 for each passenger, according to ICE.
The flights became a key piece of Border Patrol enforcement in Arizona as the agency moved to end its decades-old, revolving-door policy of taking migrants to the nearest border crossing to try again hours later.
Doris Meissner, who headed the former U.S. Immigration and Naturalization Service in the 1990s, said the pilot program was an encouraging sign that that two governments are working together to address the large number of deportees in Mexico's northern border cities.
"It makes it less likely these people will try to renter the U.S. ... and it creates some chance that they are in an environment where they actually have some ties," she said.