Fire services were struggling to put out the billowing blaze at a riverside port in Pati on the northern coast of Java island.
"We are still trying to put out the fire so that it doesn't burn more boats," spokesman for the National Disaster Management Agency, Sutopo Purwo Nugroho, said.
Three people were seriously injured in the incident, Nugroho added.
It is not clear what caused the fire. Boat accidents are common in Indonesia, a vast network of islands that relies heavily on water transport.