At least 78 people were feared dead -- most of them killed in a single landslide in the Karanganyar district that buried a late-night dinner party, a rescue official said. The victims had just cleaned up a mud-covered home.
"They were having dinner together when they were hit by another landslide," search and rescue chief Eko Prayitno said. "At least 61 people were buried."
In nearby Wonogiri district, 17 people were feared dead when landslides hit their homes following a half-day of nonstop rain.
Hundreds of soldiers, police and volunteers struggled to get heavy-lifting equipment to villages on the main island of Java, but roads blocked by the mud and flooding were hampering the rescue efforts, Prayitno said.
Lacking the equipment, some rescuers tried searching for survivors by digging into the mud with their bare hands.
Thousands of houses were inundated Wednesday, from Java to Sumatra to Sulawesi island, further east, witnesses and media reports said. Some of the fleeing residents tried salvaging their possessions from the rising waters by using tires to float their televisions and refrigerators to higher ground.
A tsunami warning drill on Java was unaffected by Wednesday's landslides.
Seasonal rains and high tides in recent days have caused widespread flooding across much of Indonesia, the world's fourth most-populous nation.
The latest disasters occurred on the third anniversary of a massive earthquake off Sumatra in December 2004 that triggered a tsunami. That killed more than 230,000 people and left a half-million homeless in a dozen countries.