Prosecutors said Kim Han-Sik, chief executive of Chonghaejin Marine Co, was taken into custody at his home and would be formally arraigned later in the day.
"Kim faces various charges including manslaughter and violating maritime law," senior prosecutor Yang Jung-Jin told AFP.
The charges stem from allegations that Kim was involved in, or turned a blind eye to, the overloading of the 6,825-tonne ferry's cargo consignment - seen as a major contributing factor to its capsize.
"I apologise to the victims and the families," he said.
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He then refused to answer further questions from reporters, staying silent with his head bowed.
The captain of the Sewol ferry has already been arrested along with 14 crew members and four lower-ranking Chonghaejin Marine officials.
The ferry had 476 people on board when it sank April 16 after listing sharply to one side and then rolling over.
Initial investigations suggest it was carrying up to three times its safe cargo capacity.
Spokesman for the federal disaster force, Ko Myung-Sok, said operations to recover the remaining bodies had been repeatedly suspended because of the conditions, with powerful currents a constant danger for the dive teams.
"So far, 24 divers have been treated for injuries and decompression sickness," Ko said.
The death of a diver on Tuesday has fuelled debate as to how long the recovery operation should continue.
The deciding factor so far has been the sensitivities of the relatives of those still unaccounted for.
The coastguard has promised that the giant floating cranes to be used in the salvage operation will only be brought in once all the bodies trapped in the submerged ship have been retrieved.