The boat carried 17 persons and overturned after it departed from a port in Tanjung Pinang of Riau province, Xinhua quoted navy spokesman Admiral Edi Sucipto as saying.
Bad weather was blamed for the disaster, he said.
Navy command in western Indonesia undertook the evacuation just after the incident, Sucipto said.
Two passengers are in critical condition and shifted to the navy hospital in the province, Sucipto added.
Search and rescue operation for the missing passengers is underway, he said.
Indonesia's 255 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.
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