An inter-island boat with 20 passengers on board sank late afternoon after high waves and strong winds lashed the eight-metre (26-foot) long boat in Maluku province.
"Eleven people have been rescued alive but nine others including two children are missing," provincial search and rescue team head Amin Bin Tongke told AFP, adding that the search operation would resume on Sunday.
"If they don't have life jackets, I'm afraid they have drowned in the rough sea," he said, adding the accident happened about four miles from the port of Tulehu.
Indonesia's 240 million people are spread across 17,000 islands and are heavily dependent on a network of ships and boats, which have a poor safety record.