The south-Asian tsunami killed 1,000 teachers and destroyed 420 schools in the Aceh province of Indonesia, the country's government has confirmed.
Many children stayed away from Guegajah school's reopening
Ministers have promised to re-start education as soon as possible, using tents and mosques as classrooms.
Unicef, the UN children's agency, is sending mobile schools to the area.
More than 150,000 people died in southern Asia and east Africa from the waves on 26 December and up to five million have been left homeless.
At Guegajah elementary school in Aceh Besar - two miles west of Aceh's capital, Banda Aceh - only half the 130 regular students attended the reopening, although most had survived the effects of the tsunami.
"There are great reasons not to go to school," said Unicef spokesman Gordon Weiss. "It's well-founded terror. The kids are in deep shock."
Aceh was the scene of some of the worst destruction, and rescue workers are still pulling bodies from the rubble, more than two weeks after the disaster, caused by an undersea earthquake measuring nine on the Richter scale.
ACEH: KEY FACTS
Province on the north-western tip of Sumatra
Higher percentage of Muslims than other parts of Indonesia
Gam rebels have fought decades-long separatist campaign
Year-long military crackdown beginning in May 2003 weakened Gam, but failed to capture senior members
At Guegajah school, displaced people crowded four classrooms, and another 3,000 were living in a nearby field.
An aftershock which registered 6.2 on the Richter scale on Monday was said to have contributed to children staying away from school.
Meanwhile, children in Sweden returned to school on Monday after the holidays to find the chairs of some classmates empty, as almost 2,000 Swedes remain missing.
In Stockholm, at least 10 elementary schools have pupils who are dead or missing.
Fifty-two Swedes have been confirmed dead after the tsunami but that number is expected to rise. A total of 637 are confirmed missing, and another 1,200 are unaccounted for.
Schools across the country are to hold a minute's silence on Wednesday at 0900 GMT.