The manifest recorded 227 passengers for the voyage to Bangka island off Sumatra, 500 km north of
Bambang Kuncoko, the national police spokesman, said: "The number of passengers is more than what was declared in the manifest, so we are still checking the exact numbers of people still missing."
He said 281 people had been rescued so far, adding: "We are still searching for more survivors."
The Antara news agency and Indonesian television reported that five navy ships were keeping up the search for survivors.
The ferry's skipper and four crew members are under police investigation.
Hatta Rajasa, the transport minister, was quoted by Antara as saying that the fire appeared to have been sparked by one of the lorries on the ferry's car deck.
Kunto Prayogo, the chief investigator, said it appeared to have been fueled by chemicals carried by the lorry "because when it was sprayed with water, it did not get smaller but bigger".
A series of Indonesian transport accidents have killed more than 450 people in two months.
Lax enforcement of safety regulations, poor maintenance and a lack of investment in transport infrastructure have been blamed for the air, sea and rail accidents, which have become a regular occurrence.
Ferries are a crucial link between the archipelago nation's 17,000 islands and frequently carry more people than officially acknowledged.