It was the latest in series of aftershocks following two major quakes on 13 February and 13 January in which at least 1,000 people died and more than one million people were left homeless.
The latest tremor, which measured 5.1 on the Richter scale, struck on Saturday spreading panic and triggering landslides. No fatalities have been reported.
It was the latest in series of aftershocks following two major quakes on 13 February and 13 January in which at least 1,000 people died and more than one million people were left homeless.
The BBC's Fiona Werge says the need for aid has become all the more urgent as El Salvador's rainy season is due to start soon.
Damage from the January quake alone is estimated to be at least $1.3 bn - over 15% of the country's annual economic output.
Following the latest tremor, President Flores appeared on radio and television urging residents of the capital, San Salvador, to remain calm.
"I want to tell the residents of the capital that I am near you, maintaining a state of continuous alert with a monitoring operation," he said.
Reports of rumbling
The latest quake's epicentre was about three miles (5km) from San Salvador, along a fault line in the San Hasinto hill.
"It felt very strong, and then I saw a big dust cloud on the volcano," said Jose Canizales, from Canton Alvarez, a small village on the slopes of the volcano overlooking the capital.
People living close to the hillsides on the south side of the city have been reporting rumbling sounds coming from inside since last Tuesday's earthquake.
There were reports of three landslides at communities in the east of the country. Several main roads are reported to have been cut off.
However, Red Cross and emergency officials said earlier reports of people trapped under landslides have proved to be untrue.
Although damage from the latest tremor appears to be relatively light, El Salvador's devastated roads, communications and water supplies have yet to be repaired.
The country has still to recover from the damage caused by Hurricane Mitch three years ago, and just in time to wreck President Flores economic reforms.