More than 200 people were killed and 2,000 injured in the second earthquake to hit El Salvador this year.
President Francisco Flores has called for urgent efforts to rescue hundreds of trapped people.
In the town of Cojutepeque several children are reported to have died when schools collapsed.
After the tremor six nursery school pupils aged between four and six, and their 25-year-old teacher, were killed when their school collapsed in Candelaria.
Teacher Ms Anabel Chavez was found with her arms wrapped around some of the children. About 40 other pupils were injured.
The quake, measuring 6.1 on the Richter scale, compares to the 7.6 quake last month that killed 844, injured 4,723 and destroyed 278,000 houses.
The quake is centred in several provinces east of the capital San Salvador.
President Flores took a helicopter tour to assess the damage to the country of six million people.
"It is true that this is another blow for El Salvador but I call for tranquillity. We have to be calm," he said.
He has said the quake's impact on the affected towns "is greater than what happened on January 13th".
PA