Prosecutors are seeking an arrest warrant for Lee Joon Seok who was in command of the 6,586-gt Sewol (built 1994) on the fateful voyage from Incheon to Jeju Island.
No details of the charges that are in prospect have yet been disclosed by investigators who are also seeking the arrest of two other officers.
Prosecutor, Park Jae Eok, indicates he wants to know why Capt Lee left the bridge of the ferry before the disaster and also question the third officer who was at the helm about events leading up to the capsize and sinking of the Sewol.
The arrest move comes as floating cranes arrived at the Sewol wreck site to begin efforts to recover the vessel which has now slipped below the waves although the vessel is attached to giant airbags.
Details of the charges facing Capt Lee have not yet been made public.
The master had earlier said he was "really sorry and deeply ashamed" about the tragic loss of the Sewol.
Survivors allege they were told to stay on the ship while Capt Lee and other crew members took to the lifeboats.
Meanwhile a deputy principal of the school where many of the missing passengers were pupils was found hanging from a tree after committing suicide.
Kang Min-kyu said in a suicide note that he felt guilty for being alive when many of his students had perished.
There are now 28 confirmed dead, 174 survivors with about 270 missing.
