Ministry spokesman Col. Erick Escobedo said 12 families initially "invaded" the land in January and the encampment had grown to 32 homes.
Escobedo said Wednesday that the country's National Coordinator for Disaster Reduction determined the encampment should be removed because the land was unstable and could cause a human disaster.
The disaster agency didn't return telephone calls from The Associated Press. An AP photographer at the site counted more than 100 families.
Escobedo said a judge ordered an eviction on Monday, but the families continued to stay.
Such evictions are controversial in the Central American country, where many of the poor live on land with disputed ownership.