The migrants, mostly from Haiti and other Latin American countries, were removed from the southern city of Tapachula by buses and taken to other states.
The migrants had been in the city while waiting for asylum and visa requests to be processed by authorities.
Migrant rights activist Luis Carcia Villagran labelled the city a “prison” as they were unable to leave without the correct paperwork.
Two groups of migrants had left in caravans headed north in recent weeks, according to Reuters,
The transfers began on Wednesday night with 120 Haitian migrants taken to the states of Aguascalientes, Campeche and Durango, say officials.
Other migrants are expected to be taken to Puebla and Guanajuato states, where they will be able to continue their applications, the official from Mexico’s national migration institute said.
INM official Hector Martinez in Tapachula told migrants that 20 buses would leave the city on Thursday.
“I’m happy, because I’m going to another city where I can work to help my family,” said Haitian immigrant Wilguens Antoine as he got set to leave Tapachula.
Similar migrant transfers also took place in the town of Mapastepec in Chiapas on Tuesday, with migrants agreeing to leave the route in exchange for Mexican visas.