The Virgo Transport 8 ferry was carrying 243 people, including 30 crew and an unknown number of vehicles, when it capsized in bad weather early on September 13 during a voyage from Surabaya in East Java to Banjarmasin in South Kalimantan.
Coast guard and Navy personnel recovered 16 bodies from inside the ship during the past three days, with nine found on Wednesday.
Two more bodies had washed ashore about 250km from the location of the accident, head of National Rescue Agency Mohammad Syafii said.
As of Wednesday, the total confirmed death toll was 28, with 107 people still missing.
There were 108 known survivors.
Search and rescue operations have been extended until September 27.
Authorities said efforts to right the ship were underway, but it remained capsized on Wednesday.
Wednesday's search focused on looking for more bodies in the ship's cabins, said I Putu Sudayana, head of the Banjarmasin rescue agency.
Divers broke the windows of the cabins on Tuesday but could not enter due to murky water and strong currents, making it impossible to retrieve bodies that had been spotted.
"Our underwater search is focused on the ship's hull. That is where we are concentrating because we have found many passengers trapped inside the cabins," he said.
After that, if possible, rescuers will shift the search to the vehicles on the ferry, but it could prove challenging, with many appearing to be piled on top of each other.
"This poses risks to the diving team," Putu said.
"If it is feasible and safe, we will carry out the search."
