The Virgo Transport 8, carrying 243 passengers and crew, had lost contact with its shipping company early on Sunday after departing from Surabaya in East Java.
“We can inform you that the total number of evacuated passengers is 103 people,” local search and rescue chief I Putu Sudayana said.
One of the passengers had died, he told reporters in the port city of Banjarmasin, where the vessel was headed.
Rescuers battled waves of up to 2.5 metres (8.2 feet) to reach the ferry, he added.
“It is extremely risky for vessels. Even our Basarnas vessel, which is 40 metres long, is at great risk,” he said, referring to Indonesia’s Search and Rescue Agency.
A Basarnas helicopter has joined the operation, he added.
Sudayana earlier told AFP that the ship’s captain had reported that the vessel was “tilting” before losing contact.
The vessel’s last position had been detected in the Java Sea, around 150 kilometres (93 miles) from its destination.
Heri Purwanto, head of the Banjarmasin Sea Port Authority, said the ship, which was carrying people and vehicles, lost contact at 2:00 am Sunday (1800 GMT Saturday).
“We responded quickly to the incident report… Our main focus and top priority at this time is the safety of everyone on board the ship, and we are deploying a coordinated rescue operation,” Heri Purwanto added.
Rescue authorities have put up a command centre at the Banjarmasin port, with paramedics and ambulances on standby, an AFP reporter saw.
Dozens of relatives and friends of the passengers checked a whiteboard where the names of people rescued were being updated.
Jenah, 26, told AFP she came to the command post for information about her older brother.
“I am saddened and very shocked. Until now, I haven’t received any more information,” said Jenah, who like many Indonesians, has only one name.
“He was travelling alone. I hope he survives. I couldn’t contact him since last night.”
Marine accidents are a regular occurrence in Indonesia — an archipelago of more than 17,000 islands that relies heavily on boat connections for daily transport and tourism.
Lax safety standards and unpredictable weather are the main reasons for the disasters.
On Monday, a speedboat carrying eight people, including five journalists working for local and international news agencies, went missing near a volcano, Mount Anak Krakatau, in Banten province and a search is ongoing.
The journalists were sent to cover the volcano’s eruption that paralysed Jakarta’s main airport and several others.
Last month, a fire on board a ferry killed one person and left five others missing while 211 were rescued in the Lombok Strait off Indonesia’s Bali island.
The ferry had been heading from Bali to Lombok when it ran into trouble in the early hours of August 12.
In July, a ferry transporting more than 70 people sank while sailing near Selayar, a small island south of Sulawesi.
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