Navy, coast guard and civilian divers were working to recover bodies from cabins on decks three and four and from a cafeteria on deck three of the Sewol, the Yonhap News Agency reported.
The first distress call from the Sewol did not come from the crew but from a boy using a mobile phone, CNN reported, citing South Korea's coast guard.
"Help us. The boat is sinking," the boy reportedly told dispatchers for the fire brigade.
The crew's first distress call was made three minutes later, the coast guard said.
The ship capsized and sank on April 16 off South Korea's south-west coast on a journey between Incheon near Seoul and the resort island of Jeju.
The actions of the ship's crew have come under scrutiny with several members, including the captain, being arrested.
Rescue efforts are now a recovery and identification effort, Yonhap reported.
The last survivor was found on the day the vessel sank.
The search continues for the missing passengers of a South Korean ferry that capsized last week, as 185 people remain unaccounted for. (Reuters video)