"Divers broke through the window of a passenger cabin just before midnight and pulled out three bodies," a coastguard official told AFP on Sunday.
All three were wearing lifejackets, the official said, adding that two were male while the gender of the third was not immediately confirmed.
They were the same three bodies that had been spotted, but not retrieved, during an earlier dive.
The confirmed death toll from the disaster now stands at 36 with 266 people still unaccounted for.
Investigators on Saturday arrested the captain accused of abandoning the South Korean ferry that capsized three days ago with 476 people on board, as divers finally accessed the submerged vessel and spotted bodies inside.
Lee Joon-Seok and two of his crew were taken into police custody and charged with negligence and failing to secure the safety of passengers in violation of maritime law.
South Korean relatives of a victim of a capsized ferry react during a funeral service in Incheon, west of Seoul. (AFP Photo)
A high school vice-principal rescued from the sinking South Korean ferry that sank with hundreds of his students on board said that he felt responsible for the disaster in an apparent suicide not. He was found dead on Friday. The vice-principal was the leader of the students travelling on a school excursion.
Local police on Jindo Island said the body of vice-principal Kang Min-Kyu, 52, was found near the gymnasium where relatives of the 268 people still missing from the ferry disaster have been staying.
“Surviving alone is too painful... I take full responsibility. I pushed ahead with the school trip,” the police quoted the note as saying. “Burn my body and scatter my ashes at the site of the sunken ferry. Perhaps I can become a teacher for the missing students in my next life,” it added.
Police said the cause of death was still under investigation, but multiple local media reports said he had been found hanging by his belt from a tree.
Of the 476 people on board the ferry when it capsized Wednesday morning, 352 were students from Danwon High School in Ansan city just south of Seoul.
They were taking the ferry for a school excursion to the popular southern resort island of Jeju. The vice-principal was among 179 people who managed to escape the ferry in the few hours before it capsized and sank.
The 69-year-old captain has been severely criticised for abandoning his ship as it sank Wednesday morning off the southwest coast while hundreds remained trapped on board, most of them children on a high school holiday trip.
Watch: Captain of sunken South Korean ferry arrested
As the arrests were being made, dive teams who had spent two days vainly battling powerful currents and near zero visibility, finally penetrated the passenger decks of the 6,825-tonne Sewol.
"Civilian divers spotted three bodies through a window," said Choi Sang-Hwan, deputy director of the national coastguard.
Many of the more than 500 divers working on the rescue teams are civilian volunteers.
Nets will be placed around the submerged ferry to prevent any bodies drifting away during the eventual recovery process, Choi said, while adding that the rescue teams had not given up hope of finding survivors trapped in air pockets.
Captain Lee was arraigned along with the two officers in charge of the bridge at the time.
Dressed in dark raincoats with their hoods pulled up, the three kept their heads bowed as they were paraded before TV cameras in a police station.
Questioned by TV reporters as to why passengers had been ordered not to move for more than 40 minutes after the ship first foundered, Lee said it was a safety measure.
Read: Bodies found trapped inside sunken South Korean ferry
Relatives watch underwater footage of divers reaching the the sunken South Korean ferry 'Sewol' at a gymnasium used as a gathering point for family members of missing passengers, in Jindo. (AFP Photo)
Captain explains evacuation delay
"At the time a rescue ship had not arrived. There were also no fishing boats around for rescues, or other ships to help," Lee said.
"The currents were very strong and the water was cold at that time in the area.
"I thought that passengers would be swept far away and fall into trouble if they evacuated thoughtlessly," he added.
Experts have suggested many more people might have escaped if they had moved to reach evacuation points before the ship listed sharply and water started flooding in.
Lee also confirmed he was not the helm when the ship ran into trouble, and was returning to the bridge from his cabin.
The hundreds of relatives camped out in a gymnasium on Jindo island near the scene of the disaster -- most of the them parents of high school students -- have sharply criticised the pace of the rescue operation, accusing officials of incompetence and indifference.
Only 174 were rescued when the ferry sank and no new survivors have been found since Wednesday.
Nam Sung-Won, whose 17-year-old nephew was among the missing, said the clock was fast running down on the hope that some may have survived.
"We don't have much time. Many people here believe this is the last possible day for finding trapped passengers alive.
Read: Vice-principal in ferry mishap commits suicide
'No hope after today'
"After today, hope will be gone," Nam said.
The unfolding tragedy was compounded by the apparent suicide Friday of the students' high school vice principal, Kang Min-Kyu, who was seemingly overcome by guilt at having survived the sinking.
Kang, 52, was found hanging from a tree near the Jindo gymnasium. Local media said he had left a note, saying: "Surviving alone is too painful... I take full responsibility."
More than 350 of those on board were students from Kang's Danwon High School in Ansan city just south of Seoul.
Initial questioning of the captain has focused on what actually caused the ferry to sink.
Tracking data from the Maritime Ministry showed the vessel made a sharp turn just before sending its first distress signal.
Some experts believe a tight turn could have dislodged the heavy cargo manifest -- including more than 150 vehicles -- and destabilised the vessel, causing it to list heavily and then capsize.
But others suggested the turn might have been caused by a collision with a rock or other submerged object.
Chief prosecutor Lee Seong-Yoon stressed there was "no limit" to the range of the investigation.
"We will make sure... those responsible are sternly held accountable," Lee said.
Three giant, floating cranes are now at the rescue site, but coastguard officials stressed they would not begin lifting the multi-deck ferry until they were sure there were no survivors inside.