The migrants had also refused to join the government’s support program, which allows applicants to receive access to job opportunities, education and medical care, the ministry said in a communique on Wednesday.
The migrants come from several caravans marching through the Mexican territory toward the United States in a hope to settle there.
Bartolo Fuentes, the migrants' leader, said earlier on Wednesday that the group was considering the offer of Mexican President Andres Manuel Lopez Obrador to stay in the country and join the Mexican labor force.
The situation around the migrants moving in the direction of the United States sparked concerns in Washington. US President Donald Trump labeled the crisis a national emergency and vowed to deploy additional troops to the Mexican border in order to prevent the migrants from crossing it.