The local government scrambled to provide food, shelter and medicine to more than 5400 people made homeless by the flooding in Jember district, about 900km east of Jakarta.
Heavy rains at the weekend triggered flash floods that sent mud, water and logs crashing into villages late on Sunday and early on Monday, destroying hundreds of buildings.
A survivor, Jumiin, who goes by only one name, said: "I thought it was the end of the world when the floods attacked houses and shops in my village."
Survivors were staying in schools, mosques and government buildings in Jember district, in the east of the country's main island of Java.
Digging for survivors
Edi Susilo, a local government spokesman, said: "Emergency supplies, including rice and noodles, have been sent to the refugees, and they will be treated by paramedics as needed."
Police, villagers and student volunteers had recovered the bodies of 57 people by early Tuesday, Susilo said.
Two villages, home to about 500
people, were cut off by the flood
He said it was likely that the death toll would rise.
Burhanudin, a local official, said rescuers were still trying to reach two villages that are home to about 500 people and were cut off by the flooding.
It was unknown how badly they were affected by the waters, said Burhanudin, who goes by a single name.
Heavy tropical downpours cause dozens of landslides and flash floods each year in Indonesia, where millions live in mountainous regions and close to rivers.