John Vandermeer of the University of Michigan says the current outbreak of the defoliating disease, known as coffee rust, is the worst seen in those regions since the fungal disease arrived there more than 40 years ago.
Guatemala recently joined Honduras and Costa Rica in declaring national emergencies, and Guatemala's president said the outbreak could cut coffee production by 40 percent in his country for the 2013-14 growing season, which could drive up the price of a cup of coffee worldwide.
Vandermeer says modern growing methods may be at the root of the problem.
Many Latin American coffee farmers have abandoned traditional shade-growing techniques, he said, in which the plants are grown beneath a diverse canopy of trees, instead converting acreage to "sun coffee," which involves thinning or removing the canopy and relying on pesticides and fungicides to keep pests in check.
However, he explained, the move to sun coffee results in a breakdown of the ecological web found on shade plantations, and the use of fungicides also results in the loss of a beneficial variety known as white halo fungus, which attacks insects and also helps keep coffee rust fungus in check.
"What we feel has been happening is that gradually the integrity of this once-complicated ecosystem has been slowly breaking down, which is what happens when you try to grow coffee like corn," Vandermeer said in a university release Tuesday.
"The path this disease takes will have huge implications for the region's coffee producers," he said.