El Salvador's Interior Minister Mario Duran said on Sunday that heavy rains from storm Amanda made rivers overflow, flooding city streets and producing landslides.
More than 7,000 people were scattered across 154 shelters, after a quarter of the rain that the country normally receives in a year fell in 70 hours.
“We’ve seen people asking for help, asking for the Government," said Mr Duran. "We haven’t deployed everywhere, the situation is overwhelming."
Among those killed was an eight-year-old boy, who died after the house he was in collapsed.
On Sunday evening, the US National Hurricane Center warned heavy rainfall could “cause life-threatening flash floods and mudslides across portions of Central America and southern Mexico, and these threats will continue over the next several days even after Amanda is no longer a tropical cyclone."
President Nayib Bukele visited one of the most affected communities on the outskirts of San Salvador. Some 50 families lost their homes and Mr Bukele said the Government would give them funding to rebuild.
One woman whose home was damaged, Maria Torres, said: “We’ve never experienced this. The rain was so strong and suddenly the water entered the homes and we just saw how they fell.”
The Legislative Assembly approved the government’s use of a 389 million dollar loan from the International Monetary Fund to deal with the pandemic and the storm’s impact.
El Salvador reports more than 2,500 infections and 46 deaths from Covid-19.
In Guatemala, a nine-year-old boy was swept away by a river and drowned and another person was killed when a home collapsed, said David de Leon, spokesman for the national disaster agency.
Amanda pounded El Salvador with rain for days before moving ashore as a tropical storm on Sunday and pushing across Guatemala.
It quickly dissipated, but the US National Hurricane Centre has said its remnants might form another storm in the Gulf of Mexico in coming days.