Authorities said 91 people were listed as missing, after the Al Khoziny school building collapsed while pupils held late afternoon prayers in a mosque housed on a lower floor of a building whose upper floors were under construction.
The boarding school is in the East Java town of Sidoarjo, about 780km east of Jakarta.
By late evening on Tuesday, three bodies had been recovered, with the vast majority of presumed victims still trapped under huge slabs of concrete. Ninety-nine children and workers at the school survived.
Holy Abdullah Arif, 49, wept as he held up a picture on his mobile phone of his nephew Rosi, still listed among the missing. He described his frantic search for the boy in the ruins.
"I ran around screaming, 'Rosi! Rosi! If you can hear me and can move, get out!' And then a child was screaming back from the rubble, he was stuck. I thought that was Rosi, so I asked, 'Are you Rosi?' and the child said, 'God, no, help me!'."
Families clustered around a whiteboard with a list of the known survivors, searching for names of their children.
An excavator and a crane had been deployed to help rescuers shift the rubble, but Nanang Sigit, a local search and rescue official, said authorities would not use heavy equipment for fear of causing the remaining structure to collapse.
"The rescuers are still searching for 91 people," spokesperson of the disaster mitigation agency Abdul Muhari told Reuters, adding that 26 of the injured were still being treated at local hospitals.
The disaster mitigation agency said the building's foundations may not have been able to support the weight of construction on its fourth floor.
The Antara state news agency quoted school caretaker Abdus Salam Mujib as saying building work had ended for the day before the prayers but that the foundations could not support the construction that had taken place on the floors above.
