0124 GMT July 23, 2018
Among the victims of Cyclone Cempaka were 25 people killed by a single landslide in east Java last week, the agency said, according to AFP.
The initial cyclone death toll was 19.
Some 28,000 people have been displaced by the storm, which hit Indonesia's most populous island last week.
"Almost five thousand homes have been damaged and more than three thousand others were inundated by flooding," said agency spokesman Sutopo Purwo Nugroho.
The destruction from the cyclone came as the rumbling Mount Agung volcano, on the neighboring resort island of Bali, threatened to erupt, forcing tens of thousands to flee their homes.
Cempaka has moved away from Indonesia, but Nugroho warned that more flooding and landslides could still happen.
Indonesia is prone to natural disasters and is often hit by floods and landslides.
A landslide on Bali in February killed 12 people, including three children. In September last year, almost 30 people died in devastating floods and landslides in Garut, West Java.