(Adds comments from crew)
By James Pearson and Kahyun Yang
SEOUL, April 24 (Reuters) - A South Korean boy whose shaking voice first raised the alarm that an overloaded ferry with hundreds of children on board was sinking has been found drowned in the submerged wreckage of the vessel, his parents believe, the coastguard said on Thursday.
The parents had seen his body and clothes and concluded he was their son, but he has not been formally identified with a DNA test.
More than 300 people, most of them students and teachers from the Danwon High School, are dead or missing presumed dead after the April 16 disaster.
The Sewol, weighing almost 7,000 tons, sank on a routine trip from the port of Incheon, near Seoul, to the southern holiday island of Jeju. Investigations are focused on human error and mechanical failure.
Of the 476 passengers and crew on board, 339 were children and teachers from the school in Ansan, a gritty suburb on the outskirts of Seoul, who were on an outing to Jeju.
As the ferry began sinking, the crew told the children to stay in their cabins.
Most of those who obeyed died. Many of those who flouted or did not hear the instructions and went out on deck were rescued.
But only 174 people were saved and the remainder are presumed to have drowned.
Classes at the school resumed on Thursday with banks of floral tributes surrounding photos of each of the victims, dressed in their school uniforms. Almost 250 teenagers and teachers at the school have died or are presumed dead.
Fellow students filed past, offering white chrysanthemums in sombre tributes.
In the classrooms of the missing, friends posted messages on desks, blackboards and windows, in the days after disaster struck, asking for the safe return of their friends.
"If I see you again, I'll tell you I love you, because I haven't said it to you enough," read one.
The school provided therapy sessions for the children as they returned.
The first distress call from the sinking vessel was made by a boy with a shaking voice, three minutes after the vessel made its fateful last turn, a fire service officer told Reuters.
The boy called the emergency 119 number which put him through to the fire service, which in turn forwarded him to the coastguard two minutes later. That was followed by about 20 other calls from children on board the ship to the emergency number.
"Save us! We're on a ship and I think it's sinking," Yonhap news agency quoted the boy as saying.
The fire service official asked him to switch the phone to the captain, media said, and the boy replied: "Do you mean teacher?"
The pronunciation of the words for "captain" and "teacher" is similar in Korean.
The ship, 146 metres (479 feet) long and 22 metres wide, was over three times overloaded, according to official recommendations, with cargo poorly stowed and inadequate ballast.
Moon Ki-han, an executive at Uryeon (Union Transport Co.), the firm that supervised cargo loading, told Reuters there were 105 containers onboard, some of which toppled into the sea as the ship listed.
Forty-five were loaded on to the front deck and 60 into the lower decks, Moon said. In total, the ship was carrying 3,600 metric tons of cargo including containers, vehicles and other goods, he said.
A member of parliament this week said the Korean Register of Shipping recommended a load of 987 tons for the Sewol.
Captain Lee Joon-seok, 69, and other crew members who abandoned ship have been arrested on negligence charges. Lee was also charged with undertaking an "excessive change of course without slowing down".
One crew member said on Thursday she and six colleagues were "under command" to abandon ship.
The unidentified crew member, speaking briefly to reporters on the way from court back into detention, was hidden behind a surgical mask and wearing a baseball cap with a jacket hood. She did not elaborate.
Another crew member was asked if there was any discussion about trying to save the passengers.
"At that moment, we were on the 3rd floor and except for the 3rd floor situation, we weren't aware of anything else," the crew member said.
The confirmed death toll from the ship on Thursday was 159, with many of those found at the back of the ship on the fourth deck.
Recovery work on Thursday was concentrated on the third and fourth decks at the front of the ship with about 700 divers, working in shifts, and an extra 36 fishing boats involved, an official told a briefing.
Helping divers were drones and a crab-like robot, called a "crabster", which can feel for bodies along the seabed.
Divers have been swimming through the dark, cold waters in the ferry, feeling for bodies with their hands.
"We are trained for hostile environments, but it's hard to be brave when we meet bodies in dark water," said diver Hwang Dae-sik.
(Additional reporting by Meeyoung Cho, Miyoung Kim, Sohee Kim an Ju-min Park; Writing by Nick Macfie; Editing by Raju Gopalakrishnan)