The KMP Tunu Pratama Jaya sank almost half an hour after leaving East Java province's Banyuwangi port on its way to Bali late on Wednesday, the agency said on Thursday.

The boat was carrying 53 passengers and 12 crew members, as well as 22 vehicles, the agency said.

A search for the missing is underway although it is being hampered by strong currents and winds, the agency said, adding it had deployed a helicopter to the location and 13 underwater rescuers.

Video provided by the Basarnas showed what appeared to be the body of one person being carried to shore from a fishing boat in calm seas.

There has been no official statement on the nationalities of the passengers, but a manifest list broadcast by news channel MetroTV indicated there were no foreigners on board.

President Prabowo Subianto, who was on a trip to Saudi Arabia, ordered an immediate emergency response, cabinet secretary Teddy Indra Wijaya said in a statement Thursday, adding the cause of the accident was "bad weather".

Java-based Surabaya search and rescue agency head Nanang Sigit, who had earlier put the total number of missing at 38, said efforts to reach the doomed vessel were initially hampered by adverse weather conditions.

Waves as high as 2.5 metres (8 feet) with "strong winds and strong currents" had affected the rescue operation, he said, adding conditions have since improved.  

A rescue team of at least 54 personnel including from the navy and police were dispatched along with inflatable rescue boats, he said, while a bigger vessel was later sent from Surabaya city to assist the search efforts. 

Ferries are a common mode of transport in Indonesia and accidents are common as lax safety standards often allow vessels to be overloaded without adequate life-saving equipment.

A small ferry capsized in 2023 near Sulawesi, killing at least 15 people.

In March, a boat carrying 16 people capsized in rough waters off Bali, killing an Australian woman and injuring at least one other person.

A ferry carrying more than 800 people ran aground in shallow waters off East Nusa Tenggara province in 2022 and remained stuck for two days before being dislodged with no one hurt.

And in 2018, more than 150 people drowned when a ferry sank in one of the world's deepest lakes on Sumatra island.