Two navigators and an engineer have also been charged, and if found guilty the foursome could be given the death penalty.
They stand accused of leaving the ship sinking whilst telling passengers to stay put, despite making their own escape.
Most of the passengers on board the vessel were students on a school trip.
Prosecutors have also charged the 11 other surviving crew members with negligence and for abandoning passengers in need.
Shocking footage has emerged since the incident, showing students dutifully staying put as the ferry lists dangerously to the side. Loudspeakers can be heard in the background reinforcing the message that they should not move from their position.
Prosecutor Ahn Sang-don said that the ferry's stability was compromised because it was overloaded on the day it set sail, April 16. He added that it also had insufficient water in the ballast tanks to keep it steady.
Captain Lee Joon-seok told passengers to stay in their cabins, despite him escaping on one of the first lifeboats.
Later, a damning image showing the captain climbing about a life raft was broadcast to the world's media.
The death toll now stands at 281, with 23 people still missing.