Five others were reported missing in the waters of a vast archipelago that relies heavily on boat transport but has a poor safety record.
In the first incident, a wooden boat in Majalengka district flipped over on a river as it carried 22 people who were mostly farmers heading to harvest their crops.
Nine people died and 13 survived, local police spokesman Yusri Yunus told AFP. Authorities were still investigating what caused the accident, he said.
In the second accident, two people died and rescuers were searching for five others missing after a passenger boat capsized in the sea off the coast of Sidoarjo district.
Boat accidents are common in Indonesia.
In January, 23 Indonesian tourists were killed when a massive fire erupted in a boat carrying hundreds of people to an island north of Jakarta to celebrate the New Year.
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