Nearly 20,000 houses, over 60 health facilities and two bridges were damaged by the flood, Sutopo Purwo Nugroho, spokesman of the national disaster management agency, told Xinhua.
The flood also cut communication and electricity supply which hampered emergency relief efforts, the spokesman said.
"Authorities have to apply'shut and open' at our main airport," Agung Pramuja, a senior official of provincial disaster agency, said.
An emergency period has been declared for 14 days until Jan. 4, said Sutopo.
The spokesman said the number of affected could rise as assessment of the flooding was underway.
Soldiers, police and rescuers from disaster agency office were taking part in the emergency relief operation, he said.