Tens of thousands of people across the region remain in emergency shelters three days after Agatha hit into western Guatemala, causing more than one metre of rain in places and raising concern over the coffee crop there and in El Salvador.
The European Union has announced $3.6m of humanitarian aid for the countries hit.
"When disaster strikes, action must be taken rapidly, be well targeted and based on needs," Kristalina Georgieva, the European humanitarian aid commissioner, said on Tuesday.
"With the aid we are allocating today we are making an immediate gesture of European solidarity for the people of the region."
She stressed that the EU will continue to monitor the situation closely, "in case further needs arise."
Ludwin Ovalle, the Guatemalan health minister, said outbreaks of dengue and
malaria were likely in the coming days.
"We will see outbreaks because of stagnant water," he said.
At least 152 people have died in Guatemala, either killed as their homes collapsed or swept away by swollen rivers.
About 100 others were missing, according to the government.
The rain has stopped in the capital, Guatemala City, but giant sinkholes created death traps on streets, swallowing entire buildings as they opened up.
In El Salvador, around 11,000 people have been evacuated to shelters.
Gerson Martinez, the transportation minister, said about 95 per cent of roads were affected by landslides, but they remained open for public use.
He also said 179 bridges had been damaged.
Meanwhile, Jorge Melendez, the director of El Salvador's civil protection agency, said the Lempa River, which flows to the Pacific, had overflowed its banks and flooded at least 20 villages.
Flooding and landslides also destroyed 505 homes in Honduras, prompting authorities to evacuate more than 2,000 people.