The small wooden vessel, which was holding more than double its capacity of about 20 people, went down yesterday as it travelled back from Panjang island to a beach in Central Java province.
Thirty-four people were plucked to safety from waters off the main island of Java and sustained only minor injuries, according to local search and rescue official Agung Hari Prabowo.
But search teams found eight bodies immediately after the accident and five more today, he said. There were three children among the dead.
The travellers had been performing a ceremony to mark the end of the Muslim Eid al-Fitr holiday, which comes after the fasting month of Ramadan.
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It involved putting an offering of a buffalo head into the sea to ask for good fortune and express thanks to God.
The Eid holiday fell last week in Indonesia, which has the world's biggest Muslim population, but many people are still off work and celebrating.
Indonesia's 240 million people are spread across more than 17,000 islands and are heavily dependent on boats for transport, but the country has a poor maritime safety record.