Lee Joon-seok, 69, was arrested with two crew members on Friday.
Divers saw three bodies in the ship on Saturday but were not able to retrieve them. The number of missing stands at 270 with 32 now confirmed dead, after three bodies were found in the water.
The official leading the rescue said it “may last one or two months.”
Some 174 passengers were rescued, but poor visibility and strong currents are making the search – now in its fourth day – difficult.
Captain Lee Joon-seok faces charges including negligence of duty and violation of maritime law after being criticized for not giving orders to evacuate soon enough.
Meanwhile relatives of the victims have begun providing DNA samples to help identify bodies recovered from the wreckage.
Investigations are focusing on a sharp turn the vessel took before it started listing and whether an evacuation order could have saved lives.
The ferry Sewol was sailing from Incheon, in the north-west, to the southern resort island of Jeju. It capsized and sank within two hours.
Lee Joon-seok, who had already been questioned by police, was shown on television on Saturday after his arrest.
“I am sorry to the people of South Korea for causing a disturbance and I bow my head in apology to the families of the victims,” he said.
“I gave instructions regarding the route, then I briefly went to the bedroom and then [the sinking] happened.
“The current was very strong, the temperature of the ocean water was cold, and I thought that if people left the ferry without proper judgement, if they were not wearing a life jacket, and even if they were, they would drift away and face many other difficulties,” he said.
He added that rescue boats had not arrived at the time of capsizing.
The helmsman at the time, Cho Joon-ki, was also among those arrested. He said that the ship reacted differently to what he had expected.
“There was a mistake on my behalf as well but the steering [gear of the ship] turned further than it was supposed to,” he told reporters.
According to documents seen by the Associated Press news agency, maritime safety officials recommended a full evacuation of the ship five minutes after a distress call was raised.
But a crew member told the agency that it took the captain 30 minutes to issue the order.
Some experts believe the ship’s tight turn could have dislodged heavy cargo and destabilized the vessel, while others suggest the sinking could have been caused by a collision with a rock.
Messages and phone calls from those inside painted a picture of people trapped in crowded corridors, unable to escape the sharply-listing ferry.
Officials say air has been pumped into the ship to aid any people trapped inside and to help refloat the vessel.
The South Korean coastguard said on Saturday that a civilian diver had seen three bodies through a window in the fourth floor of the ship.
The diver was not able to retrieve the bodies because of floating objects and time restrictions on diving, the coastguard said.
But three other bodies found in the water near the wreck were recovered, bringing the number of confirmed dead to 32.
Choi Sang-hwan, deputy director of the national coastguard, said nets would be placed around the sunken ferry to prevent any bodies drifting away.
Some 350 of those on board were students from Danwon High School in Ansan, a suburb of Seoul, who were on a school outing when the ferry sank.
Hundreds of relatives of those on board have been camping at a gymnasium on Jindo island near the scene of the disaster.
Asked how long the rescue operation was likely to continue, Shin Won-Nam, the head of the Emergency Management Centre, told reporters that it could take weeks, if not months.
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