Abdullah al-Qubaisi, from the Al-Dana company that owned the vessel which sank on Thursday, will be held for seven days for questioning "on charges of unintentional murder and unintentionally causing injury", Nawaf Hamza told reporters.
Fifty-eight people, mostly Indians and Britons, died when the traditional boat known as banoosh sank off the Gulf island state.
Seventy-two people survived the disaster.
The boat had been chartered for a company trip by corporations involved in a construction project in Bahrain. Officials said the boat had been carrying 126 people; tourism sources said it had a capacity of 100.
On Saturday, a spokesman for the interior ministry said that the boat had not been licensed to sail.