Colombian authorities had reported two new outbreaks of the disease in the Department of Cundinamarca, a large region that surrounds the capital, Bogotá.
The region has six dairy plants that export products to Mexico.
SENASICA said it acted after the World Organisation for Animal Health (OIE) removed Colombia from its list of FMD free zone countries.
The agency said it decided to take action in accordance with national and international regulations aimed at protecting the agrifood heritage of Mexico, with respect to diseases that do not exist in the country, and which could potentially jeopardize food production in Mexico.
The suspension covers the import of all milk and milk products, through the withdrawal of authorization of exporting plants, effectively resulting in a ban on importation of all dairy products originating from Colombia.