El Salvador's Environment Minister Fernando Lopez said the deluge was a result of low pressure over the Pacific Ocean, with indirect influence from tropical storm Alberto which left four people dead in Mexico.
"Unfortunately, the death toll has now reached 19, a very regrettable event," said El Salvador civil protection boss Luis Amaya, in a television interview.
Among those killed were two girls whose home was buried by a landslide.
Amaya said several preventative evacuations have been carried out in high-risk areas on hillsides and near rivers which have overflowed.
In neighboring Guatemala, authorities reported seven deaths have been recorded and said flooding had damaged roads and bridges.
The Honduras Permanent Commission for Contingencies (Copeco) reported one death, with 3,500 people affected and more than 200 homes damaged.
Several communities are cut off due to rising rivers in southern Honduras near the border with El Salvador, according to an AFP journalist.
No deaths have been reported in Nicaragua, but authorities warn of rising rivers, flooded homes and damage to roads.
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