The Virgo Transport 8 was carrying 243 people on a 20-hour voyage from Surabaya in East Java to Banjarmasin in South Kalimantan when it capsized in bad weather early on Sunday.
Six people died and 108 survived, tallies that have not changed since Sunday.
The national rescue agency and Indonesian Navy will make an assessment on Thursday on the plan to turn the capsized ship back over, including what equipment was needed, the agency's chief Mohammad Syafii told a press conference late on Wednesday.
"We plan to salvage the vessel by turning it upright and then conduct the search and evacuation. Once we are certain the operation is complete, the ship will be towed away for the investigation," Syafii said, adding local and foreign experts had been consulted.
Turning the ship upright would normally take about 24 hours, but it could take longer if "there are complications," he said.
On Wednesday, two Navy teams started an underwater search but were forced to withdraw because the current was moving at nearly seven knots, Syafii said, adding that diving is recommended only when the current is below 1.5 knots.
Some evidence discovered during the dives will be given to the National Transportation Safety Committee, which is investigating the incident, said Galih Nurna Putra, the Navy commander in Banjarmasin, without providing further details of what was found.
Air and sea surface searches on Wednesday did not find any of the 129 people still missing, Syafii said.
Similar air and surface searches will take place on Thursday.
The ship capsized around 80 nautical miles (150km) from Banjarmasin port, and it has since moved around 450m and is in waters that are around 30m deep, Syafii said.
According to Indonesia's Maritime Law, the ship's owner is required to remove or tow it if it disrupts shipping lanes.
