The South Korean ferry that sank off the country's coast on Wednesday, with the likely loss of more than 300 passengers, was being steered by an inexperienced young officer who was navigating the area, which is notorious for its fast currents, for the first time.

The revelation lends weight to the theory that a series of errors by senior crew members caused the Sewol to list and capsize, prompting a major rescue operation and questions about safety measures as South Korea struggled to with one of the worst maritime disasters in its history.

The crew appeared underprepared to deal with a serious incident at sea amid reports that the vessel's owner, Chonghaejin, had not given them guidance in how to execute a swift evacuation. There were not enough life jackets to go around, and footage of the aftermath showed that only two of more than 40 lifeboats had been deployed.

Officials said early on Sunday that divers had retrieved the first victims from inside the sunken ferry. After days of failing to gain entry to the passenger section of the ship, the South Korean team emerged with three bodies.

"At 11.48pm [2.48pm GMT], the joint rescue team broke a glass window and succeeded in getting inside the vessel," the South Korean government said in a statement. The discovery of the bodies brought to 46 the confirmed death toll from what looks to be South Korea's deadliest maritime accident in 21 years.

South Koreans awoke on Saturday to the news that the ship's embattled captain, Lee Joon-seok, had been arrested, along with the third mate, 25-year-old Park Han-kyul, who was steering the vessel at the time of the accident, and helmsman Cho Joon-ki, 55.

While Park's possible role in the accident has yet to be established, she was guiding the ship through unfamiliar waters dotted with tiny islands when the accident occurred, apparently after the ship made a sharp turn. A more experienced officer would usually have been at the wheel at that point, but Park was given control because the ship's departure on Tuesday had been delayed by heavy fog.

The ship's 69-year-old captain faces five charges, including negligence and violations of maritime law, amid accusations that he abandoned the stricken vessel while hundreds of passengers were still on board. "The captain and two crew members abandoned the ship and didn't do what they were supposed to do," said prosecutor Lee Bong-chang. "They should have also sailed more carefully without making sharp turns."

Lee, his head bowed and obscured by a grey hooded sweatshirt, told reporters during his arraignment that he had delayed evacuating the boat due to rough seas and the absence of rescue boats. Explaining why he had ordered passengers to stay put, even as the ship went into a severe list, he said: "At the time a rescue ship had not arrived. There were also no fishing boats around to rescue [us] or other ships to help.

"The currents were very strong and water was cold at that time in the area. I thought that passengers would be swept far away and get into trouble if they evacuated without wearing life jackets. It would have been the same even if they had worn life jackets."

Some survivors have disputed claims by crew members that an evacuation order was issued 30 minutes after the accident, saying they did not hear any orders to leave the ship over the public address system. On Saturday, officials confirmed that Lee had been in his private cabin when the accident occurred and had left the vessel in Park's hands.

Lee's arrest came before hundreds of divers began a fourth day searching for signs of life inside the Sewol, submerged off the coast of Jindo, a island where hundreds of relatives are following every twist and turn of the rescue operation. The vessel had left the western port on Incheon on Tuesday evening with 475 people aboard, including 325 pupils and 15 teachers from Danwon high school in the Seoul suburb of Ansan.

Tracking data shows it took a sharp, and so far unexplained, turn before sending its first distress signal. Some experts believe the turn could have dislodged heavy cargo – including more than 150 vehicles – and destabilised the vessel, causing it to list and sink. Less than two hours later, it was almost completely submerged.

As of early Sunday morning, 46 people had been confirmed dead, with 265 are missing. Officials said 174 had been rescued immediately after the accident, including 20 of the 30 crew members. The failure to rescue any passengers once the ship had sunk, or to recover most of the bodies inside, has prompted furious outbursts, and occasional scuffles, among relatives packed inside a gymnasium near the rescue operations centre on Jindo.

A woman whose child is among those missing called for the ship to be lifted out of the water so the bodies could be retrieved, and demanded that the South Korean president, Park Geun-hye, personally accompany them through their ordeal.

Mounting evidence that human error on the ship's bridge may have caused the accident has only added to the relatives' distress.

The chaotic official response to the accident was in evidence as early as Wednesday, when officials initially said all passengers had been rescued, only to backtrack and warn anxious families that almost 300 people were still unaccounted for.

Wildly conflicting reports from government agencies over the severity of the accident prompted critical comment on South Korea's ability to deal with disasters. As one poster on the popular internet portal Naver asked: "What's the point of having the world's fastest internet, coolest smartphones and the best shipbuilding industry when you can't pull that ship out of water and save our kids?"

Another said: "I thought our country was more developed than countries like Indonesia and Bangladesh, but maybe I was wrong."

As news filtered through to the presidential Blue House that the accident was worse than it had initially appeared, ministry officials struggled to establish a clear chain of command, according to South Korean media reports. The government's emergency response centre, they noted, was not launched until the crisis was into its second day.

Some wondered if the haphazard response to the accident had punctured South Korea's image of itself as a developed economy, transformed from an impoverished, war-ravaged nation in the early 1950s to an industrial and technological powerhouse through the sheer hard work and self-belief of its people.

The Kookmin Ilbo newspaper described the response as "typical of an underdeveloped country", mired in confusion, haste and delays. The Hankook Ilbo added it voice to the growing criticism, saying: "The government's easygoing reaction and internal disorder is a serious problem."

Vessels equipped with cranes have been moved to the accident site, but there were no immediate plans to use them to lift the vessel from the seabed.

Kim Jae-in, a spokesman for the South Korean coastguard, said the cranes would be used only when divers were sure lifting the vessel would not endanger anyone left alive inside: "Lifting the ship does not mean they will remove it completely from the sea. They can lift it two to three metres off the seabed."

Divers have been tapping on ship's hull in the vain hope of a response from inside, but have heard nothing. In a discovery that lends weight to the theory that the ship may have veered too quickly off course, investigators said divers had found no evidence that it had struck a rock or other submerged object.

As more than 600 divers, working in shifts, battled strong tides and poor visibility, South Korea appeared paralysed by grief. Concerts and cultural events were postponed indefinitely, while primetime dramas and variety shows gave way to occasionally melodramatic coverage of the tragedy.