Medical centres throughout the country, already overwhelmed by the thousands injured in last month's quake, are struggling to care for the additional victims.
Taken together with January's earthquake, in which more than a million lost their homes, a quarter of the population of the country are now believed to be without shelter.
At least 283 people died and nearly 3,000 were injured on Tuesday as the quake struck 15km (10 miles) south-east of the capital, San Salvador.
Medical centres throughout the country, already overwhelmed by the thousands injured in last month's quake, are struggling to care for the additional victims.
The government of El Salvador has made an urgent appeal for international aid as hospitals find themselves critically short of beds, blood and medicine.
And rescue teams trying to reach communities cut off by landslides have called for more helicopters and excavating machinery to dig out victims.
Vice President Carlos Quintanilla said the international aid received so far was insufficient.
''We can't do it with just the resources of the state and Salvadorans,'' he said.
The French news agency AFP said that the rapid response to January's earthquake has not been repeated, possibly because the earthquake in the Indian state of Gujarat in the intervening period had strained international resources.
Tuesday's tremor hit as people in El Salvador were trying to re-build their lives after last month's earthquake, which left more than 1,000 dead and caused $1bn worth of damage.
At 6.1 on the Richter scale, it was smaller than January's quake but caused huge damage because its epicentre was on land rather than under the ocean.
In one of the worst-hit villages, Candelaria in central El Salvador, at least 39 people were killed and 1,300 houses were destroyed.
Rescue workers pulled out the bodies of five small children from the wreckage of the local school.
As least 22 children and their 25-year-old teacher - found with her arms wrapped around some of the children - died there, say the authorities.