Lee Joon-seok, who is said to have left a junior officer at the helm, had been a fugitive since The Sewol went down off the South Korean holiday island of Jeju on Wednesday.
Meanwhile, Kang Min-gyu, the vice-principal of a high school, who accompanied hundreds of his pupils on the ship, has committed suicide.
A warrant had been out for Mr Joon-seok and his colleagues who are accused of failing in their duty.
One of the vessel's helmsmen, Young-seok, said of the veteran skipper: "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."
Maritime author Ju Hi-chun, who had interviewed the captain added: "I don't know why he abandoned the ship like that. 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."
Handing over the helm is normal practice on the 13-and-a-half-hour voyage from the north-western port of Incheon to the holiday island of Jeju.
The ferry went down in calm conditions and was on a frequently travelled route in familiar waters. Hopes have faded of finding any of the 274 missing alive in The Sewol, which was carrying 476 passengers and crew when it capsized on Wednesday on a journey from the port of Incheon to the southern holiday island of Jeju. There are 28 confirmed dead.
Mr Min-gyu, 52, deputy head of Danwon High School near Seoul, whose pupils were on a holiday trip, had been missing since Thursday. He appeared to have hanged himself with his belt from a tree outside a gym in the city of Jindo where relatives of the people missing on the ship, mostly children, were gathered. Police said Mr Kang did not leave a suicide note and that he was rescued from the ferry after it capsized.
The investigation into the sinking of Sewol has focused on the ferry's sharp turn before it started listing, and on whether a quicker evacuation by the captain could have saved lives. Investigators also were determining whether the captain had abandoned the ship.
The Sewol left Incheon on Tuesday on an overnight journey to Jeju in the south with 476 people on board, including 323 students from Danwon High School in Ansan. It capsized within hours of the crew making a distress call to the shore at 9am local time on Wednesday.
By last night even its blue keel had disappeared, and rescuers set two giant buoys to mark the area. Navy divers attached underwater air bags to the 6852-tonne ferry to prevent it from sinking deeper.
They are fighting strong tides and murky waters to get to the ship.
At the school, on the outskirts of Seoul, many friends and family of the missing gathered in silence.
"When I first received the call telling me the news, I still had hope," said Cho Kyung-mi, who was waiting for news of her missing 16 year-old nephew. "Now it's all gone."
In the classrooms of the missing, students have left messages on desks, blackboards and windows.
"If I see you again, I'll tell you I love you, because I haven't said it to you enough," reads one message.
It is South Korea's worst maritime accident in 21 years.