The program, which was supposed to start six months ago, will only operate for two months this year before it ends and both governments study the results, the Los Angeles Times reported Wednesday.
It was instituted for humanitarian reasons to avoid deporting people to violent border regions of Mexico.
The first flight of the Interior Repatriation Initiative landed 131 immigrants in Mexico City Tuesday. Because of the late start, flights will operate only in October and November.
Under the accord with Mexico, the United States pays for the flights and the Mexican government provides bus fare for the migrants' trips home.
U.S. and Mexican officials have not provided any specific reasons for the initiative's delay.
Mexico's Interior Ministry said more than 2,400 people would be repatriated through the program.