The first flight, which carried 131 immigrants, on October 2012, landed in Mexico City, six months after the originally scheduled start date of the program. Slated to run from April through November, the Interior Repatriation Initiative will operate only in October and November.
When the program was announced in February, Mexico's interior secretary, Alejandro Poire, said the flights would improve border security and make it easier for illegal immigrants to return to their hometowns by taking buses from the capital.
Deportees also would no longer be "systematically placed at the mercy of criminal groups in border areas," Poire said in a statement. The flights serve U.S. interests by making it harder for deportees to cross back into the U.S.
Under terms of the agreement, the U.S. pays for the flights, which depart from El Paso, and the Mexican government provides bus fares for the migrants' trips home.
U.S. and Mexican officials did not give specific reasons for the initiative's delay and limited duration.
"Given the complexities and logistics involved with this initiative, the length of time needed to launch the inaugural flight was not unreasonable," the Department of Homeland Security said in a statement.
The Mexican Interior Ministry confirmed the arrival of the first flight at Mexico City's international airport in October, and said the program would continue through Nov. 29, transporting more than 2,400 people.
"Once in national territory, they will be given food and ground transportation to their communities of origin and-or residence in Mexico," the ministry and the National Migration Institute said in a statement. It said the arriving Mexicans would be given a list of social services available to them and allowed to request medical attention, as well as a phone call to their families.
If there are outstanding criminal charges in Mexico against any of the passengers, they will be investigated for possible prosecution, the ministry said.
Repatriating illegal immigrants has become problematic in recent years as deportations reach record highs and besieged border areas struggle to provide security and housing for people who often arrive penniless and without any contacts.
In the northeastern state of Tamaulipas, where deportations have surged fivefold in recent years, criminals prey on deportees, sometimes abducting them from streets, bus stations and migrant shelters. Many are held for ransom, and others are recruited into criminal networks that have seized control of much of the region.