The ferry had been towed towards the harbour from the site of the fire about 60 nautical miles away.
The death toll from the initial fire on rose to 50 by Tuesday after two bodies were found late on Monday afternoon, said Rotman, an official at Tanjung Priok.
The total number of confirmed dead following the fire and sinking stands at 53.
Estimates put the number of people missing at between 50 and 100.
At least four navy warships continued to comb waters east of where the ferry caught fire to look for those still missing from the initial disaster, Rotman added.
Estimates suggest more than 350 people were on the vessel when fire broke out. About 250 people were rescued.
Police have detained the ferry's skipper and first officer on suspicion of negligence and making false declarations in official documents.
The government has already revoked the ferry operator's permit for declaring fewer passengers on its manifest than it was actually carrying.