Rescuers were searching through wrecked houses and mounds of earth for 15 villagers still missing after days of rain triggered the landslips and flash floods on mountainous Java island over the weekend.
They were using excavators to hunt for survivors in more accessible areas, and in more remote places were digging through debris with their bare hands and shovels.
Disaster agency spokesman Sutopo Purwo Nugroho said 47 people were confirmed dead, 15 were missing and 14 had suffered injuries.
Hundreds of homes were badly damaged, with some completely flattened.
He said a La Nina weather system, which typically causes unseasonably heavy rains, could have contributed to the flooding.
Java, which should be entering the dry season, has been hit by torrential downpours in recent weeks.
"This June there's still heavy rainfall which is causing floods and landslides," Mr Nugroho said, warning La Nina was set to strengthen in the coming months, increasing the risk of disasters.
Indonesia and other parts of Asia had been affected by a strong El Nino, which brings drought and sizzling temperatures.
La Nina often follows an El Nino phenomenon.
Mr Nugroho also blamed inadequate preparations, saying his agency had warned local authorities that heavy rains were coming but it was not clear if they had taken action.
Evacuation centres, equipped with temporary shelters and kitchens, have been set up near the disaster zones.