President Otto Molina Perez also has ordered the release of more than $14 million to aid coffee growers.
He says the funds are aimed at helping 60,000 small farmers to buy pesticides and to teach them how to prevent the disease and stop it from spreading.
Molina said Friday that the pesticides will start being applied to coffee plants in April and that two more applications will be needed during the year.
Coffee rust is currently affecting plantations in Mexico, Guatemala, El Salvador, Honduras and Costa Rica.
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