The KM Mutiara Sentosa ferry, carrying 271 passengers, was travelling from Indonesia's second-largest city of Surabaya in East Java province to Makassar city in South Sulawesi before it caught fire on Sunday, authorities had said.
Madura island is located off the northeastern coast of Java.
Arman Asmara Syarifuddin, director of marine and air affairs at East Java police, said that of the 271 people on board, 28 remain missing, with five confirmed dead and 238 rescued.
"Police with the rescue agency and the Navy have deployed seven boats and one helicopter to find the missing people," Arman said on Monday.
The seven boats deployed included one naval corvette, speed boats, and a patrol boat capable of carrying around 100 passengers, he added.
The rescuers are focusing their search on an area extending 16km to the east and 16km to the west of the location of the incident.
The search operation would last for seven days but could be extended another 14 days, Arman said.
The cause of the incident remains unclear.
All the rescued victims were evacuated to the Port of Gapura Surya Nusantara in Surabaya on Monday morning.
Families of the victims had been anxiously waiting at the port since Sunday evening.
Indonesia, an archipelago of around 17,000 islands, relies heavily on ferries as a key mode of transportation, with sea routes more affordable and readily available than air travel.
However, safety standards are not always strictly enforced, and accidents are relatively frequent.
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