So far, about 600 bodies have been recovered, but officials say the final number of dead will exceed 1,000.
Two strong tremors were felt on Tuesday, triggering landslides and damaging buildings already weakened by Saturday's 7.6 magnitude quake.
The authorities had already begun moving people away from the danger zones, as thousands spent their third night outdoors.
So far, about 600 bodies have been recovered, but officials say the final number of dead will exceed 1,000.
The continued seismic activity is sparking panic among survivors.
"Everyone is so tense. As soon as anything starts to shake, you run out. It's really frightening," said office cleaner Sonia Calderon.
President Francisco Flores said the worst was over, but that some of the hardest-hit areas were still at risk.
Nearly 18,000 people have been evacuated from dangerous zones, police said.
Survivor ill
Nearly three days after the quake struck, the authorities have switched their attention from rescue to relief.
The dead are being buried as quickly as possible, often in mass graves.
It is now more than 36 hours since the last survivor was pulled from under the mud and rubble and he is fighting for his life.
Sergio Moreno was rescued on Sunday after being trapped for 30 hours. He is suffering heart and kidney failure and has had a leg amputated.
A Red Cross spokesman said rescue efforts were expected to continue for at least another 24 hours, but the priorities were providing food and shelter for survivors.
The quake left more than 45,000 homes destroyed or damaged and major roads blocked.
As many as half of the country's six million people are without water supplies, the Pan-American Health Organisation said.
Efforts are being intensified to get food, blankets and tents to those made homeless.
Improvised shelters of canvas and plastic have been erected and the army is distributing rations of rice and beans.
President Flores has thanked the international community for its help in mounting a massive relief operation.
Deforestation
El Salvador's national emergency committee has said the number of dead is likely to rise as it receives full reports from rural areas.
A Red Cross spokesman, Dennis McClean, suggested the disaster had been made worse by the erosion of topsoil caused by tree felling.
"One of the contributive factors to the high loss of life in this disaster has been deforestation," he said.
Some of those who lost relatives in the badly-hit San Salvador suburb of Las Colinas have strongly criticised the authorities for allowing houses to be built in the area.
Officials told the BBC that about 500 people had been killed in the area.
The quake also hit Guatemala, Honduras, Mexico, Costa Rica and Nicaragua.
The last major earthquake in El Salvador was in 1986 when 1,400 people died.