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Yonhap said Captain Lee Joon-seok, 69, faced five charges including negligence of duty and violation of maritime law.
Investigators had said earlier that Lee was not on the bridge at the time the Sewol ferry started to list sharply on Wednesday, with a junior officer at the wheel. Arrest warrants were issued on Friday for Lee, the officer at the wheel and one other crew member for failing in their duty to aid passengers.
"I'm not sure where the captain was before the accident. However, right after the accident, I saw him rushing back into the steering house ahead of me," said Oh Young-seok, one of the helmsmen on the ship who was off duty and resting at the time.
"He calmly asked by how much the ship was tilted, and tried to re-balance the ship," said Oh, who was speaking from a hospital bed in the city of Mokpo on Friday, where the injured have been taken.
The Sewol, carrying 476 passengers and crew, capsized on Wednesday on a journey from the port of Incheon to the southern holiday island of Jeju.
Handing over the helm is normal practice on the voyage from Incheon to Jeju, which usually takes 13.5 hours, according to local shipping crew.
Divers gained access to the cargo deck of the ferry on Friday, although that was not close to the passenger quarters, according to a coastguard official.
Other coastguard officials said that divers made several attempts to reach the passenger areas but failed.
"We cannot even see the ship's white colour. Our people are just touching the hull with their hands," Kim Chun-il, a diver from Undine Marine Industries, told relatives of the missing.
The ferry went down in calm conditions and was following a frequently travelled route in familiar waters. Although relatively close to shore, the area was free of rocks and reefs.
Lee has not commented on when he left the ship, although he has apologised for the loss of life.
He was described as an industry veteran by the officials from Chonghaejin Marine Co Ltd, the ship owner, and others who had met him described him as an "expert".
"I don't know why he abandoned the ship like that," said Ju Hi-chun, a maritime author who interviewed the captain in 2006 as one of the experts on the route to Jeju island.
But he added: "Koreans don't have the view that they have to stay with their ship until the end. It is a different culture from the West."
Some media reports have said the vessel turned sharply, causing cargo to shift and the ship to list before capsizing.
Marine investigators and the coastguard have said it was too early to pinpoint a cause for the accident and declined to comment on the possibility of the cargo shifting.
The record of the ferry owner was also under investigation and documents were removed from its headquarters in Incheon.
Chonghaejin Marine Co Ltd is an unlisted company that operates five ships. It reported an operating loss of 785 million won ($756,000) last year.
According to data from South Korea's Financial Supervisory Service, a government body, Chonghaejin is "indirectly" owned by two sons of the owner of a former shipping company called Semo Marine which went bankrupt in 1997.