"Divers broke through the window of a passenger cabin just before midnight and pulled out three bodies," a coastguard official said.
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.
More From This Section
The age of the victims pulled from the ferry today night was not immediately known.
Their recovery followed days of fruitless efforts by more than 500 divers to access the submerged ship in the face of powerful currents and near-zero visibility.
Relatives of the missing gathered in the southern island of Jindo -- not far from the disaster site -- have been clinging to the slimmest of hopes that some may have survived in trapped air pockets.
All three have been criticised for abandoning hundreds of passengers still trapped in the ferry, as they made their own escape.
Lee was charged with negligence and failing to secure the safety of passengers in violation of maritime law.
All three were paraded before TV cameras at their arraignment, dressed in dark raincoats with their hoods pulled up and their heads bowed.