The indictment was filed Thursday in Gwangju District Court and a trial date will be decided in a few days, according to a court official who requested anonymity due to department rules. The official said all 15 defendants are expected to be tried together.
The indicted crew members were among the first group of people rescued when the Sewol began badly listing, and all were arrested last month.
Lee initially told passengers to stay in their cabins and took about half an hour to issue an evacuation order but it's not known if his message was ever conveyed to passengers. In a video taken by the coast guard, he was seen escaping the ferry in his underwear to a rescue boat while many passengers were still in the sinking ship.
Lee told reporters after his arrest last month that he withheld the evacuation order because rescuers had yet to arrive and he feared for the passengers' safety in the cold, swift water.
The head of the ferry's owner, Chonghaejin Marine Co. Ltd., and four other company employees have also been arrested. Authorities suspect improper stowage and overloading of cargo may have contributed to the disaster.
About one month after the sinking, 284 bodies have been retrieved and 20 others are listed as missing. Only 172 people, including 22 of the ship's 29 crew members, survived. Most of the victims were students from a single high school near Seoul who were traveling to the southern tourist island of Jeju.
Underwater searches for the bodies have been hampered by strong currents and bad weather. Family members of the missing passengers are still camping out at a nearby port waiting for news of their loved ones. One civilian diver died after falling unconscious during a search.
The sinking, one of the deadliest disasters in South Korean history, has triggered an outpouring of national grief. More than 1.8 million people have paid their respects at makeshift mourning stations across the country. The government also has been under mounting public criticism over its handling of the disaster.
Associated Press writer Youkyung Lee contributed to this report.