According to South Korean investigators, the third officer was at the helm of Sewol ferry that capsized off Jindo island.
A total of 268 people – including scores of high school students – remain missing after Wednesday’s disaster.
Twenty-eight people are now known to have died and 179 were rescued.
It is not clear why the ferry sank, but experts have suggested it either hit a rock or turned sharply, unbalancing the vessel as cargo shifted.
Sewol ferry had been travelling from Incheon, in the north-west, to the southern resort island of Jeju. It capsized and sank within a period of two hours, officials said.
A major search and rescue operation has been under way. Bad weather, poor visibility and strong currents hampered the divers’ search on Thursday.
Some of the divers have managed to enter the cargo bay of the ship, a coast guard official confirmed in a press conference on Friday.
But they could not identify or rescue any people due to items obstructing the way, the unnamed official added.
Air was also now being injected into the ship to help any people trapped inside – though officials have said that survivors are unlikely – and to help refloat the vessel.
Coast guard officials, quoted by AFP, say the bodies picked up were found floating in the water, and none had been retrieved from the ship itself.
Three salvage cranes have also arrived at the scene, to raise the ship or move it to another area with weaker currents.
“We will review the options very carefully, as the salvage operations may hurt survivors trapped inside,” Yonhap news agency quoted a coast guard officer as saying.
Meanwhile, investigators have stated that the captain of the ferry, Lee Joon-seok, was not in charge when the ferry ran into trouble.
“It was the third officer who was in command of steering the ship when the accident took place,” state prosecutor Park Jae-Eok told journalists.
“Whether or not they took a drastic turnaround… is under investigation,” he said.
“Though surviving crews have different testimonies about the situation, we’ve been investigating the captain as he was suspected to leave the steering room for an unknown reason,” Park Jae-Eok added.
In a separate development, reports say the vice principal of Danwon High School, who was rescued from the ferry, was found dead on Friday.
Yonhap news agency quotes police as saying Kang Min-Kyu, 52, was found hanging from a tree near the gym where many of the relatives of missing passengers have been staying.
Witnesses have accused the crew of telling passengers to remain where they were, rather than evacuate the sinking ship.
Messages and phone calls from those inside painted a picture of people trapped in crowded corridors, unable to escape the severely-listing ferry.
Some 350 of those on board were students from the same high school in a suburb of Seoul who were on a field trip.
Their relatives have endured a long wait for news – their anguish compounded by conflicting information about numbers of survivors issued early on.
In a public statement issued on Friday, families of the missing called for more urgent action.
“Nobody told us about what went wrong and what was happening out there. There was not even a situation room in charge by late Wednesday,” a representative said.
“Our children would be shouting for help in the freezing water,” he said.
“Please help us save our children.”
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