Parts of North Sumatra province were cut off by damaged roads and downed communications lines, and relied on relief aircraft to deliver aid supplies.
Rescue efforts were also hampered by a lack of heavy equipment.
Rescuers in North Sumatra recovered 31 bodies on Saturday, said provincial police spokesperson Ferry Walintukan, increasing the death toll to 279.
More than 3500 police were deployed to search for 174 people still missing and help distribute aid to more than 28,000 who fled to temporary government shelters across the province, he said.
Monsoon rains in the past week caused rivers to burst their banks.
The deluge tore through mountainside village, swept away people and submerged thousands of houses and buildings.
In the Agam district in West Sumatra province, nearly 80 people were missing in three villages, buried under tonnes of mud and rocks.
There was a desperate need for heavy equipment to reach possible survivors. Relatives wailed as they watched rescuers pull bodies from a buried house in Salareh Aia village.
Images also showed massive piles of logs washed ashore on West Sumatra's Air Tawar Beach, sparking public concern over possible illegal logging that may have contributed to the disaster.
In Aceh province, on the northern tip of Sumatra, authorities had difficulty deploying tractors and other heavy equipment.
Hundreds of police, soldiers and residents dug through the debris with bare hands, shovels and hoes as heavy rain pounded the region.
TV reports showed two rescuers battling strong currents in a small rubber boat, moving towards a man clinging to a coconut tree.
"There are many challenges," Aceh governor Muzakir Manaf said after declaring a state of emergency to address the disaster.
"We have to do many things soon, but conditions do not allow us to do so."
Local media said flash floods in Bireuen district in Aceh collapsed nine bridges, paralysed two-way transportation from North Sumatra's Medan city to Banda Aceh, and forced residents to cross the river from village to village by boat.
It was the latest natural disaster to hit Indonesia, which is frequently struck by earthquakes, volcanic eruptions and tsunamis because of its location on the "Ring of Fire", an arc of volcanoes and fault lines in the Pacific Basin.
Seasonal rains frequently cause flooding and landslides in Indonesia, where millions of people live in mountainous areas or near fertile flood plains.
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