The state news agency, Antara, put the number of missing at five - a journalist, two transportation safety officials and two forensic police staff - and said three others had been hospitalised.
Lieutenant-Colonel Hendra Pakan, a spokesman for the Indonesian navy's western fleet, said the scorched hulk had been hauled to a point about six to 10 miles from the main port in Jakarta.
"It had been anchored at the time, but it was tilting on one side," he said.
Agus Faisal Karim, an SCTV reporter who had been aboard the boat, said: "Some of us were given life vests, but others were not wearing (them)."
"We are safe, we are not injured, but all of us panicked. Some of us were in the water for a long time," he added.
Colonel Didin Zainal Abidin, head of the navy's rescue team, said the search for more victims and survivors of Thursday's fire was continuing.
About 300 of those who were on board are known to have survived, but how many were still missing was clouded in confusion because a number of passengers were apparently not listed on the official manifest.
Preliminary findings by investiagators suggested the fire started in a truck carrying an inflammable chemical cargo on the lower deck.
Many passengers hurled themselves off the blazing 27-year-old Japanese-built vessel into the sea to escape the flames.