The death toll from the collapse of an Islamic boarding school in Indonesia last week jumped to at least 49 people as rescuers have cleared nearly all of the debris, the country's disaster mitigation agency said in a statement handed out on Monday.

Piles of concrete caved in on hundreds of mostly teenage boys after the collapse of the Al Khoziny school in the Indonesian town of Sidoarjo, in East Java province, trapping and later killing them.

Using excavators, rescuers late on Sunday cleared 80% of the debris and found body parts of the mostly teenage victims, the agency's statement said, adding the search will continue for more victims.

Rescue officials carried orange body bags out of the ruins of the school, according to footage shared by the search and rescue agency.

The school's foundations could not support ongoing construction work on the upper floors, causing the collapse, authorities have said.

Across Indonesia, there are about 42,000 Islamic school buildings, known locally as a pesantren, data from the country's religious affairs ministry shows.

Only 50 pesantren have building permits, Dody Hanggodo, the country's public works minister, was quoted by local media as saying on Sunday.

It is not immediately clear if Al Khoziny had a building permit. Reuters could not immediately contact school authorities for comment.