Rescue teams trying to reach communities cut off by landslides have called for more helicopters and excavating machinery to dig out victims.
Government officials say they need more food aid and the Salvadoran Red Cross has again appealed for blood donations to help treat thousands of people injured by collapsing buildings.
At least 283 people died in the quake, which struck one month after another earthquake left about 1,000 people dead.
Rescue teams trying to reach communities cut off by landslides have called for more helicopters and excavating machinery to dig out victims.
More than one million people have been left homeless by the two disasters, and thousands are sleeping in the streets or makeshift shelters.
Donor fatigue warning
A UN official warned on Thursday that international aid could be affected by what he called donor fatigue in response to several natural disasters in quick succession.
"It is the consequence of a global situation where you have a recurrence of natural disasters that create distress in the capacity of the donor community to attend all these situations," he said.
His comments came as the United Nations World Food Programme said Tuesday's earthquake had given it another 100,000 mouths to feed.
But a senior presidential official in El Salvador sad he did not believe the international community was suffering from compassion, but he thought that foreign governments had not fully appreciated the impact of the second earthquake.
School victims
Tuesday's tremor hit as people in El Salvador were trying to rebuild their lives after last month's earthquake, which left more than 1,000 dead and caused damage estimated at $1bn.
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.
At least 22 children and their 25-year-old teacher - found with her arms wrapped around some of the children - died there, say the authorities.