Part of the multi-story building gave way suddenly on Monday as students gathered for afternoon prayers.

"Today we managed to evacuate seven victims, five of them were rescued alive, and two were found dead," Yudhi Bramantyo, operational director of the National Search and Rescue Agency (Basarnas), told a press briefing in Sidoarjo.

"The five survivors were able to communicate," he added.

The latest death toll brings the number of people killed in the disaster to five.

Tearful parents milled near the ruins throughout Wednesday awaiting news.

Based on school records "91 people are suspected to be buried," the National Disaster Mitigation Agency (BNPB) spokesperson Abdul Muhari said in a statement late Tuesday.

"We believe our children might still be alive because they were crying for help," said father Abdul Hanan, whose 14-year-old son is missing. "The rescue operation must be accelerated."

"We are racing against time now," the 45-year-old added, bursting into tears.

Investigations into the cause of the collapse are ongoing but initial signs point to structural issues and construction that did not meet building standards, experts said.

Dewi Sulistiana was awaiting news of her 14-year-old son she was last in touch with on Sunday. The boarding school limits student access to cellphones.

She rushed to the scene from East Java's capital of Surabaya after hearing about the collapse.

"I have been here for days. I cried thinking about my son," she told AFP. "Why is taking so long to find him, why is the search so slow? I haven't had any updates, so I just wait."

Tunnels and drones

The rescue operation is complex, said Basarnas head Mohammad Syafii.

"If vibration happens in one spot, it could affect other places. So now, to reach the spot where the victims are, we have to dig an underground tunnel," he told reporters.

Digging itself poses challenges, including possible landslides. And any tunnel will only provide an access route around 60 centimetres wide because of the structure's concrete columns.

Technology including thermal-sensing drones is being used to locate survivors and the deceased as the 72-hour "golden period" for best survival chances nears its end.

AFP saw rescuers in orange uniforms appearing to snake cameras under the rubble to hunt for traces of survivors.

So far, signs of life have been detected in seven areas, said rescue official Emi Freezer of the Basarnas.

Water and food was being sent in, but access was through a single point, he said. "The main structure has totally collapsed."

Around 59 people remain trapped under the ruins, official said Thursday.

"Data updated Wednesday at 11:00 pm indicates that 59 people are still trapped under the rubble," Abdul from the BNPB said in a statement, adding that the data was evolving as some people who survived the incident have not yet come forward.

He said the figure was based on an attendance list released by the boarding school.

Complicating the operation, an earthquake struck offshore overnight, briefly halting the search.

Around the ruins, local charitable organizations have set up posts offering families food and drink.

The school collapse was so violent it sent tremors across the neighborhood, said local resident Ani.

"I felt a vibration and then I heard a noise. I immediately ran to save myself. I didn't realize at first it was a building collapse," the grocery stall owner told AFP.

"Many people then also ran to save themselves," she added.

The building folded after its foundation pillars failed to support the weight of new construction on the fourth floor of the school, said the BNPB.

Lax construction standards have raised widespread concerns about building safety in Indonesia, where it is common to leave structures, particularly houses, partially completed, allowing owners to add extra floors later when their budgets permits.

Earlier this month, at least three people were killed and dozens injured when a building hosting a prayer recital collapsed in West Java.