The death toll from a school collapse in Indonesia climbed to 54 on Monday, with rescuers continuing to search for more than a dozen people still missing, officials said.

Part of the multi-storey building on Indonesia's Java island collapsed suddenly last week as students gathered for afternoon prayers.

As of this morning, "we have retrieved 54 dead victims, including five body parts," National Search and Rescue Agency (Basarnas) operations director Yudhi Bramantyo told a press conference.

Rescuers were still working around the clock in the rubble of the Islamic boarding school.

"We hope we can conclude the recovery today (Monday), and we will return the bodies (to the families)," Yudhi said.

The collapse was Indonesia's deadliest disaster so far this year, Budi Irawan, the deputy head of the national disaster agency (BNPB), said.

At least 13 people were still missing, he added.

Investigators have been examining the cause of the collapse, but initial indications suggest that substandard construction may have contributed to the incident, according to experts.

The families of the missing agreed on Thursday for heavy equipment to be used, after the 72-hour "golden period" for the best chance of survival came to an end.

Lax construction standards have raised widespread concerns about building safety in Indonesia.

At least three people were killed and dozens were injured in September when a building hosting a prayer recital collapsed in West Java.