A landslide killed nine people at Pacitan in East Java province and two people died in floods triggered by heavy rain in the same area.
Thousands of homes were flooded and 4,000 people forced to evacuate them, said a spokesman for the national disaster mitigation agency.
The extreme weather will continue to hit the Indonesian islands of Java and Bali, the spokesman added, warning people to be prepared for floods, landslides and tornados.
The agency said it urgently needs blankets, clothes and inflatable boats for affected areas.
Indonesia is often hit by landslides and floods.
Twelve people including three children died in a landslide on the holiday island of Bali in February.
In September last year almost 30 people died in devastating floods and landslides in Garut, West Java.
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